validation of late phase biomarkers

Setup: Libraries and utilities

Import data

latephase_exacer_biomarkers <- readRDS(here::here("results", "latephase_exacer_biomarkers.rds"))
load(here::here("data", "preprocessedData", "geodatasets.RDATA"))

## samples in each dataset
table(phenoDataList$GSE19301$phenotype)

## 
## EXACERBATION    FOLLOW UP        QUIET 
##          166          125          394

all(colnames(esetList$GSE19301) == rownames(phenoDataList$GSE19301))

## [1] TRUE

geoPanelGenes <- as.data.frame(t(esetList$GSE19301))
geoPanelGenes <- geoPanelGenes[, intersect(colnames(geoPanelGenes), latephase_exacer_biomarkers)]

geoPanelGenes <- add_column(geoPanelGenes, donor = phenoDataList$GSE19301$donor, .before = 1)
geoPanelGenes <- add_column(geoPanelGenes, sex = phenoDataList$GSE19301$sex, .before = 1)
geoPanelGenes <- add_column(geoPanelGenes, phenotype = phenoDataList$GSE19301$phenotype, .before = 1)

Exacerbation dataset (GSE19301)

mod_exacer <- run_lme(
  data = geoPanelGenes[phenoDataList$GSE19301$severity == "Moderate Persistent", ],
  fdr = 0.1
)
mod_exacer$severity <- "Moderate Persistent"

sev_exacer <- run_lme(
  data = geoPanelGenes[phenoDataList$GSE19301$severity == "Severe Persistent", ],
  fdr = 0.1
)
sev_exacer$severity <- "Severe Persistent"

exacer <- rbind(mod_exacer, sev_exacer)

Volcano plot (exacerbation contrasts)

scaleFUN <- function(x) sprintf("%.0f", x)

exacer$logPval <- -log10(exacer$`p-value`)
exacer$Sig <- ifelse(exacer$adj.P.Val < 0.1, "FDR<10%", "NotSignificant")

gg1 <- ggplot(exacer, aes(x = Value, y = logPval, color = Sig)) +
  geom_point(size = 2) +
  geom_vline(aes(xintercept = 0), lty = 2, color = "gray") +
  geom_text_repel(
    data = filter(exacer, adj.P.Val < 0.1),
    aes(label = feature),
    size = 2,
    max.overlaps = 100
  ) +
  customTheme(
    sizeStripFont = 8, xAngle = 0, hjust = 0.5, vjust = 0.5,
    xSize = 8, ySize = 8, xAxisSize = 8, yAxisSize = 8
  ) +
  scale_x_continuous(expression("log"[2]~"fold-change")) +
  scale_y_continuous(expression("-log"[10]~"P-value"), labels = scaleFUN) +
  scale_color_manual(values = c("blue", "gray")) +
  ggtitle("PBMCs - GSE19301") +
  theme(legend.position = "bottom") +
  facet_grid(contrast ~ severity, scales = "free")

gg1

Summarize significant hits (exacerbation)

exacer %>%
  group_by(severity, contrast, fc) %>%
  filter(adj.P.Val < 0.1) %>%
  summarise(n = n())

## # A tibble: 6 × 4
## # Groups:   severity, contrast [4]
##   severity            contrast          fc        n
##   <chr>               <chr>             <chr> <int>
## 1 Moderate Persistent Exacer - Followup UP        3
## 2 Moderate Persistent Exacer - Quiet    DOWN      1
## 3 Moderate Persistent Exacer - Quiet    UP        8
## 4 Severe Persistent   Exacer - Followup UP        1
## 5 Severe Persistent   Exacer - Quiet    DOWN      3
## 6 Severe Persistent   Exacer - Quiet    UP       11

exacer %>%
  group_by(severity, contrast, fc) %>%
  filter(adj.P.Val < 0.1) %>%
  filter(severity == "Severe Persistent", contrast == "Exacer - Quiet", fc == "DOWN") %>%
  pull(feature)

## [1] "CD48"    "C9orf78" "PABPC1"

External validation datasets (airway/blood/sputum/BALF)

select_gse <- c("GSE69683", "GSE74986", "GSE147878+GSE161245", "GSE76262+GSE147880")

result <- mapply(function(x, y, z, tis) {
  res <- test_biomarkers(eset = x, pheno = y, biomarkers = latephase_exacer_biomarkers)
  res$GSE <- z
  res$tissue <- tis
  res
},
x = esetList[select_gse],
y = phenoDataList[select_gse],
z = select_gse,
tis = sapply(phenoDataList[select_gse], function(i) unique(i$sampletype)),
SIMPLIFY = FALSE) %>%
  do.call(rbind, .) %>%
  mutate(fc = ifelse(logFC > 0, "UP", "DOWN"))

## number of patients
table(phenoDataList$GSE19301$severity, phenoDataList$GSE19301$phenotype)

##                      
##                       EXACERBATION FOLLOW UP QUIET
##   Mild Persistent                7         6    21
##   Moderate Persistent           68        60   180
##   Severe Persistent             91        59   193

length(unique(phenoDataList$GSE19301$donor[phenoDataList$GSE19301$severity == "Mild Persistent"]))

## [1] 7

length(unique(phenoDataList$GSE19301$donor[phenoDataList$GSE19301$severity == "Moderate Persistent"]))

## [1] 52

length(unique(phenoDataList$GSE19301$donor[phenoDataList$GSE19301$severity == "Severe Persistent"]))

## [1] 59

rowSums(sapply(phenoDataList[select_gse], function(i) table(i$phenotype)))

## healthyControls  moderateAsthma    severeAsthma 
##             159             171             548

GSE19301 individuals by sex and severity

phenoDataList$GSE19301 %>%
  filter(severity != "Mild Persistent") %>%
  group_by(donor) %>%
  dplyr::slice(1) %>%
  group_by(sex, severity) %>%
  summarise(n = n()) %>%
  tidyr::spread(sex, n) %>%
  mutate(total = `M` + `F`) %>%
  mutate(percent_f = 100 * signif(`F` / total, 2)) %>%
  mutate(total_percentf = paste0(total, " (", percent_f, "%)"))

## # A tibble: 2 × 6
##   severity                F     M total percent_f total_percentf
##   <chr>               <int> <int> <int>     <dbl> <chr>         
## 1 Moderate Persistent    36    16    52        69 52 (69%)      
## 2 Severe Persistent      39    20    59        66 59 (66%)

Validation datasets individuals by sex and phenotype

a <- data.frame(sampletype = sapply(phenoDataList[select_gse], function(i) unique(i$sampletype))) %>%
  mutate(gse = rownames(.))

b <- lapply(select_gse, function(i) {
  df <- as.data.frame(table(phenoDataList[[i]]$sex, phenoDataList[[i]]$phenotype))
  df$gse <- i
  df
}) %>%
  do.call(rbind, .) %>%
  tidyr::spread(Var1, Freq) %>%
  mutate(total = `F` + `M`) %>%
  mutate(percent_f = 100 * signif(`F` / total, 2))

inner_join(a, b, by = "gse") %>%
  mutate(gse_sample = paste0(sampletype, " (", gse, ")")) %>%
  mutate(total_percentf = paste0(total, " (", percent_f, "%)")) %>%
  dplyr::select(Var2, gse_sample, total_percentf) %>%
  tidyr::spread(gse_sample, total_percentf)

##              Var2 airway (GSE147878+GSE161245) balf (GSE74986) blood (GSE69683)
## 1 healthyControls                     29 (66%)        12 (42%)         87 (39%)
## 2  moderateAsthma                     23 (78%)        28 (57%)         77 (48%)
## 3    severeAsthma                     59 (63%)        46 (54%)        334 (61%)
##   induced sputum (GSE76262+GSE147880)
## 1                            31 (45%)
## 2                            43 (58%)
## 3                           109 (59%)

Volcano plots across validation datasets

df <- result %>%
  mutate(sig = -log10(P.Value)) %>%
  mutate(Significance = ifelse(adj.P.Val < 0.1, "FDR<10%", "NotSignificant")) %>%
  mutate(tissue_gse = paste(tissue, GSE, sep = "_"))

p <- df %>%
  ggplot(aes(x = logFC, y = sig, col = Significance)) +
  geom_point() +
  ggh4x::facet_grid2(vars(tissue_gse), vars(contrast),
                     scales = "free", independent = "all") +
  scale_color_manual(values = c("blue", "gray")) +
  ggrepel::geom_text_repel(
    data = subset(df, adj.P.Val < 0.1),
    aes(label = feature), size = 2, max.overlaps = 20
  ) +
  geom_vline(xintercept = 0, linetype = "dashed") +
  theme(legend.position = "top") +
  customTheme(
    sizeStripFont = 8, xAngle = 0, hjust = 0.5, vjust = 0.5,
    xSize = 8, ySize = 8, xAxisSize = 8, yAxisSize = 8
  ) +
  xlab(expression("log"[2]~"fold-change")) +
  ylab(expression("-log"[10]~"P-value"))

ggsave(
  here::here("results", "validation_of_late_phase_biomarkers_volcanoplots.png"),
  p, height = 11, width = 8
)

p

Summarize significant hits (external validation)

result %>%
  group_by(tissue, contrast, fc) %>%
  filter(adj.P.Val < 0.1) %>%
  summarise(n = n()) %>%
  tidyr::spread(fc, n)

## # A tibble: 11 × 4
## # Groups:   tissue, contrast [11]
##    tissue         contrast       DOWN    UP
##    <chr>          <chr>         <int> <int>
##  1 airway         mod - control     1     7
##  2 airway         sev - control     6    18
##  3 airway         sev - mod        NA     1
##  4 balf           mod - control     5    NA
##  5 balf           sev - control    33    33
##  6 balf           sev - mod        32    37
##  7 blood          sev - control     9    30
##  8 blood          sev - mod         3     9
##  9 induced sputum mod - control     1    NA
## 10 induced sputum sev - control    19    27
## 11 induced sputum sev - mod        17    18

Overlap of significant genes (UpSet)

sig_result <- subset(result, adj.P.Val < 0.1)
sig_exacer <- subset(exacer, adj.P.Val < 0.1)

df_exacer <- data.frame(
  panel = paste0(sig_exacer$contrast, " (", sig_exacer$severity, sig_exacer$tissue, "-", sig_exacer$GSE, ")"),
  feature = sig_exacer$feature
)

df_sev <- data.frame(
  panel = paste0(sig_result$contrast, " (", sig_result$tissue, "-", sig_result$GSE, ")"),
  feature = sig_result$feature
)

sigfeat1 <- split(df_exacer$feature, df_exacer$panel)
upset(fromList(sigfeat1), nsets = length(sigfeat1))

sigfeat2 <- split(df_sev$feature, df_sev$panel)
upset(fromList(sigfeat2), nsets = length(sigfeat2))

upset(fromList(c(sigfeat1, sigfeat2)), nsets = length(sigfeat1) + length(sigfeat2))

Exacerbation analysis

Train PLS-DA models (exacerbation)

latephase_biomarkers <- readRDS(here::here("results", "latephase_biomarkers.rds"))
latephase_biomarkers$all <- latephase_exacer_biomarkers
# exacer_plsda <- lapply(names(latephase_biomarkers), function(i){
#   biomarkers <- latephase_biomarkers[[i]]
#   ## all subjects
#   demo <- subset(phenoDataList$GSE19301, severity == "Moderate Persistent")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_all_mod <- multilevel_plsda(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_all_mod$df$comparison <- paste(exacer_all_mod$df$comparison, "(Moderate Persistent)")
#   exacer_all_mod$feat$comparison <- paste(exacer_all_mod$feat$comparison, "(Moderate Persistent)")
#   exacer_all_mod$df$sex <- exacer_all_mod$feat$sex <- "M+F"
#   demo <- subset(phenoDataList$GSE19301, severity == "Severe Persistent")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_all_sev <- multilevel_plsda(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_all_sev$df$comparison <- paste(exacer_all_sev$df$comparison, "(Severe Persistent)")
#     exacer_all_sev$feat$comparison <- paste(exacer_all_sev$feat$comparison, "(Severe Persistent)")
#   exacer_all_sev$df$sex <- exacer_all_sev$feat$sex <- "M+F"
# 
#   ## females
#   demo <- subset(phenoDataList$GSE19301, severity == "Moderate Persistent" & sex ==  "F")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_f_mod <- multilevel_plsda(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_f_mod$df$comparison <- paste(exacer_f_mod$df$comparison, "(Moderate Persistent)")
#   exacer_f_mod$feat$comparison <- paste(exacer_f_mod$feat$comparison, "(Moderate Persistent)")
#   exacer_f_mod$df$sex <- exacer_f_mod$feat$sex <- "F"
#   demo <- subset(phenoDataList$GSE19301, severity == "Severe Persistent" & sex ==  "F")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_f_sev <- multilevel_plsda(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_f_sev$df$comparison <- paste(exacer_f_sev$df$comp, "(Severe Persistent)")
#     exacer_f_sev$feat$comparison <- paste(exacer_f_sev$feat$comparison, "(Severe Persistent)")
#   exacer_f_sev$df$sex <- exacer_f_sev$feat$sex <- "F"
# 
#   ## males
#   demo <- subset(phenoDataList$GSE19301, severity == "Moderate Persistent" & sex ==  "M")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_m_mod <- multilevel_plsda(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_m_mod$df$comparison <- paste(exacer_m_mod$df$comparison, "(Moderate Persistent)")
#     exacer_m_mod$feat$comparison <- paste(exacer_m_mod$feat$comparison, "(Moderate Persistent)")
#   exacer_m_mod$df$sex <- exacer_m_mod$feat$sex <- "M"
#   demo <- subset(phenoDataList$GSE19301, severity == "Severe Persistent" & sex ==  "M")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_m_sev <- multilevel_plsda(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_m_sev$df$comparison <- paste(exacer_m_sev$df$comparison, "(Severe Persistent)")
#     exacer_m_sev$feat$comparison <- paste(exacer_m_sev$feat$comparison, "(Severe Persistent)")
#   exacer_m_sev$df$sex <- exacer_m_sev$feat$sex <- "M"
# 
#   exacer_df <- rbind(exacer_all_mod$df, exacer_all_sev$df,
#                   exacer_f_mod$df, exacer_f_sev$df,
#                   exacer_m_mod$df, exacer_m_sev$df)
#   exacer_feat <- rbind(exacer_all_mod$feat, exacer_all_sev$feat,
#                 exacer_f_mod$feat, exacer_f_sev$feat,
#                 exacer_m_mod$feat, exacer_m_sev$feat)
#   exacer_df$panel <- exacer_feat$panel <- i
#   list(df = exacer_df, feat = exacer_feat)
# }) %>%
#   zip_nPure()
# saveRDS(exacer_plsda, here("results", "exacer_plsda.rds"))

Train RF models (exacerbation)

# exacer_rf <- lapply(names(latephase_biomarkers), function(i){
#   biomarkers <- latephase_biomarkers[[i]]
#   ## all subjects
#   demo <- subset(phenoDataList$GSE19301, severity == "Moderate Persistent")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_all_mod <- multilevel_rf(eset = eset, demo = demo,
#                    biomarkers = biomarkers, workers = 8)
#   exacer_all_mod$df$comparison <- paste(exacer_all_mod$df$comparison , "(Moderate Persistent)")
#   exacer_all_mod$feat$comparison <- paste(exacer_all_mod$feat$comparison, "(Moderate Persistent)")
#   exacer_all_mod$df$sex <- exacer_all_mod$feat$sex <- "M+F"
#   demo <- subset(phenoDataList$GSE19301, severity == "Severe Persistent")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_all_sev <- multilevel_rf(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_all_sev$df$comparison <- paste(exacer_all_sev$df$comparison, "(Severe Persistent)")
#   exacer_all_sev$feat$comparison <- paste(exacer_all_sev$feat$comparison, "(Severe Persistent)")
#   exacer_all_sev$df$sex <- exacer_all_sev$feat$sex <- "M+F"
# 
#   ## females
#   demo <- subset(phenoDataList$GSE19301, severity == "Moderate Persistent" & sex ==  "F")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_f_mod <- multilevel_rf(eset = eset, demo = demo,
#                    biomarkers = biomarkers, workers = 8)
#   exacer_f_mod$df$comparison <- paste(exacer_f_mod$df$comparison, "(Moderate Persistent)")
#   exacer_f_mod$feat$comparison <- paste(exacer_f_mod$feat$comparison, "(Moderate Persistent)")
#   exacer_f_mod$df$sex <- exacer_f_mod$feat$sex <- "F"
#   demo <- subset(phenoDataList$GSE19301, severity == "Severe Persistent" & sex ==  "F")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_f_sev <- multilevel_rf(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_f_sev$df$comparison <- paste(exacer_f_sev$df$comparison, "(Severe Persistent)")
#   exacer_f_sev$feat$comparison <- paste(exacer_f_sev$feat$comparison, "(Severe Persistent)")
#   exacer_f_sev$df$sex <- exacer_f_sev$feat$sex <- "F"
# 
#   ## males
#   demo <- subset(phenoDataList$GSE19301, severity == "Moderate Persistent" & sex ==  "M")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_m_mod <- multilevel_rf(eset = eset, demo = demo,
#                    biomarkers = biomarkers, workers = 8)
#   exacer_m_mod$df$comparison <- paste(exacer_m_mod$df$comparison, "(Moderate Persistent)")
#   exacer_m_mod$feat$comparison <- paste(exacer_m_mod$feat$comparison, "(Moderate Persistent)")
#   exacer_m_mod$df$sex <- exacer_m_mod$feat$sex <- "M"
#   demo <- subset(phenoDataList$GSE19301, severity == "Severe Persistent" & sex ==  "M")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_m_sev <- multilevel_rf(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_m_sev$df$comparison <- paste(exacer_m_sev$df$comparison, "(Severe Persistent)")
#   exacer_m_sev$feat$comparison <- paste(exacer_m_sev$feat$comparison, "(Severe Persistent)")
#   exacer_m_sev$df$sex <- exacer_m_sev$feat$sex <- "M"
# 
#   exacer_df <- rbind(exacer_all_mod$df, exacer_all_sev$df,
#                   exacer_f_mod$df, exacer_f_sev$df,
#                   exacer_m_mod$df, exacer_m_sev$df)
#   exacer_feat <- rbind(exacer_all_mod$feat, exacer_all_sev$feat,
#                 exacer_f_mod$feat, exacer_f_sev$feat,
#                 exacer_m_mod$feat, exacer_m_sev$feat)
#   exacer_df$panel <- exacer_feat$panel <- i
#   list(df = exacer_df, feat = exacer_feat)
# }) %>%
#   zip_nPure()
# saveRDS(exacer_rf, here("results", "exacer_rf.rds"))

Plot model performance heatmap (exacerbation)

exacer_plsda <- readRDS(here("results", "exacer_plsda.rds"))
exacer_rf <- readRDS(here("results", "exacer_rf.rds"))
col_names <- intersect(colnames(exacer_rf$df[[1]]), colnames(exacer_plsda$df[[1]]))
panel_names <- c("all", "panCancer", "UCSC_isoforms", "UCSC", "Ensembl", "Trinity")
auc <- rbind(do.call(rbind, exacer_rf$df),
             do.call(rbind, exacer_plsda$df))[, col_names] %>% 
  filter(stat == "AUC.mean") %>% 
  dplyr::select(-stat) %>% 
  mutate(model_panel = paste(model, panel, sep="_")) %>% 
  dplyr::select(-c(model, panel)) %>% 
  spread(model_panel, value)

auc2 <- auc[, -c(1:4)]
classifer <- factor(sapply(strsplit(colnames(auc2), "_"), function(i) i[[1]]),
                    c("RF", "PLSDA"))
colnames(auc2) <- sapply(strsplit(colnames(auc2), "_"), function(i) i[[2]])
row_ha <- rowAnnotation(sampletype=rep("PBMCs", nrow(auc)),
                        comparison=auc$comparison, 
                        sex=auc$sex,
                        col = list(sampletype = c("PBMCs" = "red"),
                                   comparison = c("Exacer vs. Quiet (Moderate Persistent)"="#DEEBF7", "Exacer vs. Quiet (Severe Persistent)"="#9ECAE1", "Exacer vs. followup (Moderate Persistent)"="#4292C6", "Exacer vs. followup (Severe Persistent)"="#084594"),
                                   sex = c("F"="#80CDC1","M"="#35978F","M+F"="#01665E")))

h1 <- Heatmap(auc2, column_split = classifer,
        right_annotation = row_ha, 
        cluster_columns = TRUE,
        border = TRUE, name="AUC",
    cell_fun = function(j, i, x, y, width, height, fill) {
        if(auc2[i, j] > 0.9) {
          grid.text("***", x, y, gp = gpar(fontsize = 15))
        } else if(auc2[i, j] > 0.8) {
          grid.text("**", x, y, gp = gpar(fontsize = 15))
        } else if(auc2[i, j] > 0.7) {
          grid.text("*", x, y, gp = gpar(fontsize = 15))
        }
})
h1

Summarize model performance table (exacerbation)

exacertable <- rbind(do.call(rbind, exacer_plsda$df)[, col_names], 
                     do.call(rbind, exacer_rf$df)[, col_names]) %>% 
  mutate(value = signif(value, 2)) %>%  
  filter(stat == "AUC.mean") %>% 
  spread(model, value) %>% 
  filter(PLSDA > 0.7) %>% 
  filter(RF > 0.7)
write.csv(exacertable, here::here("results", "exacerbation_models_perfs.csv"))

knitr::kable(exacertable)

gse	sampletype	comparison	stat	sex	panel	PLSDA	RF
GSE19301	blood	Exacer vs. followup (Moderate Persistent)	AUC.mean	M	all	0.96	0.87
GSE19301	blood	Exacer vs. followup (Moderate Persistent)	AUC.mean	M	Ensembl	0.89	0.76
GSE19301	blood	Exacer vs. followup (Moderate Persistent)	AUC.mean	M	panCancer	0.94	0.85
GSE19301	blood	Exacer vs. followup (Moderate Persistent)	AUC.mean	M	Trinity	0.88	0.89
GSE19301	blood	Exacer vs. followup (Moderate Persistent)	AUC.mean	M	UCSC	0.96	0.83
GSE19301	blood	Exacer vs. followup (Moderate Persistent)	AUC.mean	M	UCSC_isoforms	0.88	0.84
GSE19301	blood	Exacer vs. followup (Moderate Persistent)	AUC.mean	M+F	all	0.79	0.75
GSE19301	blood	Exacer vs. followup (Moderate Persistent)	AUC.mean	M+F	panCancer	0.75	0.71
GSE19301	blood	Exacer vs. followup (Moderate Persistent)	AUC.mean	M+F	UCSC_isoforms	0.71	0.71
GSE19301	blood	Exacer vs. followup (Severe Persistent)	AUC.mean	M	all	0.84	0.71
GSE19301	blood	Exacer vs. followup (Severe Persistent)	AUC.mean	M	Ensembl	0.76	0.73
GSE19301	blood	Exacer vs. followup (Severe Persistent)	AUC.mean	M+F	panCancer	0.76	0.71
GSE19301	blood	Exacer vs. Quiet (Severe Persistent)	AUC.mean	M	all	0.85	0.74
GSE19301	blood	Exacer vs. Quiet (Severe Persistent)	AUC.mean	M	Ensembl	0.83	0.77
GSE19301	blood	Exacer vs. Quiet (Severe Persistent)	AUC.mean	M	UCSC	0.82	0.74

Compile feature importance (exacerbation)

selectcols <- intersect(colnames(exacer_plsda$feat[[1]]), colnames(exacer_rf$feat[[1]]))
exacerfeat <- rbind(do.call(rbind, exacer_plsda$feat)[, selectcols], 
                     do.call(rbind, exacer_rf$feat)[,selectcols]) %>% 
  right_join(exacertable, by=c("gse", "comparison", "panel", "sex")) %>% 
  dplyr::select(-c(stat, PLSDA, RF, sampletype, gse)) %>% 
  group_by(comparison, panel, sex, model) %>%
  mutate(rank_pct = percent_rank(importance))

knitr::kable(exacerfeat)

importance	feature	comparison	model	sex	panel	rank_pct
0.0877911	ABHD5	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.0000000
1.0224415	AHCTF1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.6923077
0.8704903	ATP8A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.5000000
0.5661089	C9orf78	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.1538462
0.9756409	CARM1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.6153846
1.1376971	CASP8	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.7307692
0.8850023	CD4	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.5384615
1.5128511	CD8A	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.8846154
1.0104758	CLEC4E	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.6538462
0.5715329	DAP	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.1923077
0.1768168	F13A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.0384615
0.6461579	FAM8A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.2692308
1.3216195	FOS	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.8076923
0.8166068	FUT7	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.4230769
1.3525909	GNLY	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.8461538
1.7056172	KRT23	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.9615385
0.6704963	LMBRD1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.3461538
1.7079546	NAPA	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	1.0000000
0.6488016	NFKBIA	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.3076923
1.6797881	PABPC1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.9230769
0.6715769	PPP3R1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.3846154
0.2661511	RGS2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.0769231
0.8869331	SF3B1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.5769231
0.8357684	SH3BGRL3	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.4615385
1.2294257	SULT1A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.7692308
0.3651834	TGFBI	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.1153846
0.5836783	ZNF185	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC	0.2307692
0.4473591	ABHD5	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.1923077
1.1174415	AHCTF1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.6923077
1.4319774	ATP8A1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.9615385
1.0028204	C9orf78	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.5000000
1.0169405	CARM1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.5384615
0.3413159	CASP8	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.1153846
0.3866290	CD4	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.1538462
1.2426199	CD8A	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.7692308
1.0991658	CLEC4E	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.6538462
1.0174478	DAP	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.5769231
0.1737126	F13A1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.0384615
0.5793715	FAM8A1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.3461538
0.4692968	FOS	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.2307692
0.8601632	FUT7	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.4615385
1.3797764	GNLY	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.8846154
0.5694985	KRT23	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.3076923
1.3781785	LMBRD1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.8461538
2.0901844	NAPA	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	1.0000000
0.1372844	NFKBIA	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.0000000
1.2580091	PABPC1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.8076923
0.8493250	PPP3R1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.4230769
0.4702369	RGS2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.2692308
1.4029497	SF3B1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.9230769
1.2140191	SH3BGRL3	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.7307692
0.5982879	SULT1A1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.3846154
0.2372827	TGFBI	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.0769231
1.0884730	ZNF185	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	UCSC	0.6153846
0.1803827	ATP11A	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.0000000
0.5640095	ATP8A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.1785714
0.5872002	CD8A	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.2142857
0.8403073	CLEC4E	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.5000000
1.5279153	COPB1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.9285714
0.4505025	F13A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.1428571
0.2447460	FAM8A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.0357143
1.1248206	FPR2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.7142857
1.4593048	GNAS	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.8928571
2.1129936	GNLY	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	1.0000000
1.4006469	IL1R2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.8571429
0.9609346	MAP3K8	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.6428571
0.6829335	MME	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.4285714
1.7815826	NAPA	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.9642857
0.9417063	NFKBIA	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.5714286
1.2480459	PELI1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.8214286
1.1601356	PLXNC1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.7500000
0.6750556	PTPN18	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.3928571
0.5990098	QKI	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.2500000
0.6417218	RGS2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.3214286
0.2510591	SEMA4D	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.0714286
0.6748342	SF3B1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.3571429
0.9452884	SH3BGRL3	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.6071429
1.1813716	SULT1A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.7857143
0.6936612	TGFBI	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.4642857
0.6195848	TIA1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.2857143
0.4245471	VCAN	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.1071429
0.8913275	VPS13A	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.5357143
0.9756126	ZNF609	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	UCSC_isoforms	0.6785714
0.4020223	ATP11A	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.1071429
0.8860436	ATP8A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.5357143
1.4396901	CD8A	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.8571429
1.3512213	CLEC4E	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.7500000
1.8213609	COPB1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	1.0000000
0.2735740	F13A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.0357143
0.6867574	FAM8A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.4642857
1.4790375	FPR2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.8928571
0.9515987	GNAS	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.6428571
1.3879264	GNLY	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.8214286
0.3212753	IL1R2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.0714286
0.2353370	MAP3K8	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.0000000
0.6838714	MME	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.4285714
1.7293257	NAPA	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.9642857
0.6415576	NFKBIA	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.3571429
0.5505922	PELI1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.2857143
1.6903877	PLXNC1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.9285714
0.9285497	PTPN18	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.5714286
0.9305672	QKI	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.6071429
0.4196255	RGS2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.1785714
0.6539878	SEMA4D	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.3928571
0.9691715	SF3B1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.6785714
0.8172215	SH3BGRL3	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.5000000
1.3625132	SULT1A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.7857143
0.6012095	TGFBI	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.3214286
0.4197238	TIA1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.2142857
1.1482195	VCAN	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.7142857
0.4099388	VPS13A	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.1428571
0.5127518	ZNF609	Exacer vs. followup (Moderate Persistent)	PLSDA	M	UCSC_isoforms	0.2500000
0.9300874	AHCTF1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.5714286
0.9322525	ATP8A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.6071429
0.5490593	C9orf78	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.2500000
0.7076325	CARM1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.3571429
1.3594702	CD8A	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.8571429
0.3741793	CHP1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.1785714
1.0960742	CISH	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.7142857
0.9440011	CLEC4E	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.6428571
0.7665829	CTDSP2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.4285714
1.8921714	CTSA	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	1.0000000
0.7512955	DAP	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.3928571
0.3160528	DESI1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.0714286
0.3474527	F13A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.1071429
0.9008612	FAM8A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.5357143
0.3685283	GBE1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.1428571
1.4086930	GNLY	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.8928571
0.6304071	ITSN1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.2857143
1.3206876	KIAA1551	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.8214286
1.8776638	KRT23	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.9642857
1.6509880	PABPC1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.9285714
0.6843379	PPP3R1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.3214286
0.8862552	RALGPS2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.5000000
0.1448315	RGS2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.0000000
1.2038069	SF3B1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.7857143
1.1198763	SH3BGRL3	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.7500000
1.0751600	SMCHD1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.6785714
0.8067201	TGFBI	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.4642857
0.1788827	ZNF185	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.0357143
0.5369857	ZNF281	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Ensembl	0.2142857
1.2834740	AHCTF1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.8214286
1.3257733	ATP8A1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.8928571
0.9523216	C9orf78	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.5357143
0.9401382	CARM1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.5000000
1.1576029	CD8A	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.7857143
0.5597433	CHP1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.1428571
1.3892372	CISH	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.9285714
1.1540047	CLEC4E	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.7500000
0.7630767	CTDSP2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.2500000
1.7030912	CTSA	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	1.0000000
0.9897867	DAP	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.5714286
1.0259112	DESI1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.6071429
0.5028171	F13A1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.0714286
0.5404799	FAM8A1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.1071429
0.0651958	GBE1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.0000000
1.4518977	GNLY	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.9642857
0.9324425	ITSN1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.4642857
0.8592535	KIAA1551	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.3928571
0.6765841	KRT23	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.2142857
1.1516170	PABPC1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.7142857
0.7905629	PPP3R1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.3571429
0.7736266	RALGPS2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.3214286
0.4888772	RGS2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.0357143
1.3149607	SF3B1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.8571429
1.1181224	SH3BGRL3	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.6785714
0.8709182	SMCHD1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.4285714
0.6035202	TGFBI	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.1785714
1.0813882	ZNF185	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.6428571
0.7689633	ZNF281	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	Ensembl	0.2857143
0.4067022	AHCTF1	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.1071429
1.2605809	ATP8A1	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.7500000
1.5819286	C9orf78	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.9642857
0.9918346	CARM1	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.5714286
0.8202338	CD8A	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.4285714
0.8173274	CHP1	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.3928571
1.9415268	CISH	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	1.0000000
1.0311537	CLEC4E	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.6428571
0.7635236	CTDSP2	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.3214286
1.3214434	CTSA	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.8571429
1.0364489	DAP	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.7142857
0.9025835	DESI1	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.5000000
1.4055280	F13A1	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.8928571
1.2712943	FAM8A1	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.7857143
0.0822397	GBE1	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.0357143
0.5296847	GNLY	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.2142857
0.9617249	ITSN1	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.5357143
0.3402024	KIAA1551	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.0714286
0.7863603	KRT23	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.3571429
0.4676326	PABPC1	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.1428571
0.4964051	PPP3R1	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.1785714
0.7052919	RALGPS2	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.2857143
0.8707276	RGS2	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.4642857
1.0331844	SF3B1	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.6785714
1.2816592	SH3BGRL3	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.8214286
0.9941773	SMCHD1	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.6071429
0.6436201	TGFBI	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.2500000
1.4126411	ZNF185	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.9285714
0.0237509	ZNF281	Exacer vs. followup (Severe Persistent)	PLSDA	M	Ensembl	0.0000000
0.9174632	CASP8	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Trinity	0.5555556
1.4732724	CECR1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Trinity	1.0000000
0.6469333	FPR1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Trinity	0.1111111
1.1591063	FPR2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Trinity	0.7777778
0.5502773	IFRD1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Trinity	0.0000000
1.0868191	LYST	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Trinity	0.6666667
0.9111520	QKI	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Trinity	0.4444444
1.2410676	SETX	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Trinity	0.8888889
0.7381732	SF3B1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Trinity	0.2222222
0.9090393	TNFRSF10C	Exacer vs. followup (Moderate Persistent)	PLSDA	M	Trinity	0.3333333
1.0169273	ARG2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.6216216
1.2071914	CD48	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.7837838
0.6053159	CD55	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.1621622
1.0147593	CDH1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.5945946
0.1807212	CREBBP	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.0270270
0.8052270	CXCL10	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.3783784
0.7140808	CXCL2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.3243243
0.6862511	CXCL6	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.2432432
0.8046177	F13A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.3513514
0.7063260	FOS	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.2972973
1.2598111	FOXJ1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.8378378
0.6010383	FUT7	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.1351351
1.8672136	IFI35	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	1.0000000
0.8532260	IL15RA	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.4324324
0.8587806	IL1R1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.4864865
0.6996183	IL26	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.2702703
1.3180710	IL32	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.8918919
1.2273357	ITGA2B	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.8108108
1.1491755	JAM3	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.7567568
0.9253242	LCN2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.5675676
1.4943660	LCP1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.9189189
1.6254987	LILRB1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.9729730
0.6849084	MAP3K5	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.2162162
1.0272311	MS4A2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.6486486
0.5688267	PLAU	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.1081081
1.0892099	PPBP	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.6756757
0.5571441	PSEN1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.0540541
1.0930164	SBNO2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.7027027
1.1001293	SELPLG	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.7297297
0.8591867	SH2B2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.5135135
0.8958020	SPINK5	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.5405405
0.1544993	TFEB	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.0000000
1.3172065	TFRC	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.8648649
0.5669270	THY1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.0810811
0.8313618	TLR7	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.4054054
1.5350921	TNFSF10	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.9459459
0.8569296	TNFSF4	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.4594595
0.6825752	ULBP2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	panCancer	0.1891892
1.5383153	ARG2	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.8648649
1.1829750	CD48	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.7837838
0.5050695	CD55	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.2432432
0.5979769	CDH1	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.3513514
0.6784124	CREBBP	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.4324324
1.0312915	CXCL10	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.6486486
0.2558693	CXCL2	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.1081081
0.1145380	CXCL6	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.0000000
1.0908750	F13A1	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.7027027
0.9911977	FOS	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.6216216
0.5801083	FOXJ1	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.2972973
0.5671567	FUT7	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.2702703
1.0628298	IFI35	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.6756757
0.7460665	IL15RA	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.4864865
0.2374816	IL1R1	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.0810811
0.7322161	IL26	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.4594595
0.4319631	IL32	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.2162162
0.7879571	ITGA2B	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.5675676
0.2118370	JAM3	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.0540541
2.2212908	LCN2	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	1.0000000
0.9536251	LCP1	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.5945946
1.7285613	LILRB1	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.9729730
0.3035852	MAP3K5	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.1351351
0.1551969	MS4A2	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.0270270
0.7653851	PLAU	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.5405405
1.1125762	PPBP	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.7297297
0.3874246	PSEN1	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.1891892
1.7025763	SBNO2	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.9189189
0.3612447	SELPLG	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.1621622
1.6288792	SH2B2	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.8918919
0.5829659	SPINK5	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.3243243
0.6451082	TFEB	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.4054054
1.7127206	TFRC	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.9459459
0.7614964	THY1	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.5135135
1.4117139	TLR7	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.8378378
1.1451823	TNFSF10	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.7567568
1.2124262	TNFSF4	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.8108108
0.6400770	ULBP2	Exacer vs. followup (Severe Persistent)	PLSDA	M+F	panCancer	0.3783784
1.1826808	ARG2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.7027027
0.5123010	CD48	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.1891892
0.3896840	CD55	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.1351351
0.9606092	CDH1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.5135135
0.4009437	CREBBP	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.1621622
1.0873882	CXCL10	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.6216216
0.3559479	CXCL2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.1081081
1.7464995	CXCL6	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	1.0000000
0.6885290	F13A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.3783784
1.0974646	FOS	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.6486486
0.2612269	FOXJ1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.0540541
0.5738559	FUT7	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.2972973
1.6778245	IFI35	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.9729730
0.6589128	IL15RA	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.3513514
0.1386748	IL1R1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.0000000
1.4289972	IL26	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.8918919
0.8784814	IL32	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.4864865
1.0134434	ITGA2B	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.5675676
1.1221671	JAM3	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.6756757
0.5299687	LCN2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.2162162
1.6440995	LCP1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.9459459
1.3461723	LILRB1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.8378378
0.6111722	MAP3K5	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.3243243
1.0228056	MS4A2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.5945946
0.2552212	PLAU	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.0270270
0.9886653	PPBP	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.5405405
1.2520930	PSEN1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.7837838
0.8627602	SBNO2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.4594595
1.4764003	SELPLG	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.9189189
1.4004986	SH2B2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.8648649
1.2001291	SPINK5	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.7297297
1.2407031	TFEB	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.7567568
0.5725011	TFRC	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.2702703
0.5388196	THY1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.2432432
0.2722379	TLR7	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.0810811
1.2729485	TNFSF10	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.8108108
0.8550295	TNFSF4	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.4324324
0.7513250	ULBP2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	panCancer	0.4054054
0.6044210	ABHD5	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.2127660
0.6837999	AHCTF1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.2978723
0.7130663	ARG2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.3404255
0.0269865	ATP11A	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.0000000
0.4327256	ATP8A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.0957447
0.8602907	C9orf78	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.4680851
0.6094054	CARM1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.2234043
0.6475334	CASP8	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.2659574
0.9392675	CD4	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.5638298
0.9967116	CD48	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.6170213
1.1626274	CD55	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.7978723
0.5072926	CD8A	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.1489362
1.0697222	CDH1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.7446809
1.8910084	CECR1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.9893617
1.0658100	CHP1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.7340426
0.6030846	CISH	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.1914894
0.8494652	CLEC4E	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.4468085
1.1104248	COPB1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.7765957
0.3306227	CREBBP	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.0531915
1.8500108	CTDSP2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.9680851
1.4534347	CTSA	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.8936170
1.0021742	CXCL10	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.6382979
1.0620763	CXCL2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.7234043
0.7110702	CXCL6	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.3297872
0.4371152	DAP	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.1063830
0.8231883	DESI1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.4255319
0.4559994	F13A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.1170213
0.2864787	FAM8A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.0319149
0.8739648	FOS	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.4893617
1.4466114	FOXJ1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.8829787
0.8722879	FPR1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.4787234
0.8900180	FPR2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.5319149
0.6889401	FUT7	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.3085106
1.2069016	GBE1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.8191489
1.2200048	GNAS	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.8297872
1.5459320	GNLY	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.9148936
2.1454943	IFI35	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	1.0000000
1.0442114	IFRD1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.6914894
0.8379855	IL15RA	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.4361702
1.0815916	IL1R1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.7553191
1.0600990	IL1R2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.7127660
0.7562684	IL26	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.3723404
1.4628293	IL32	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.9042553
0.8915369	ITGA2B	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.5425532
0.1902779	ITSN1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.0106383
1.1751169	JAM3	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.8085106
0.6914221	KIAA1551	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.3191489
0.8753571	KRT23	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.5106383
1.0570349	LCN2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.7021277
1.7247584	LCP1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.9468085
1.8729356	LILRB1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.9787234
0.8832964	LMBRD1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.5212766
0.9971940	LYST	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.6276596
0.6709763	MAP3K5	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.2765957
0.8743412	MAP3K8	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.5000000
0.9522570	MME	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.5851064
1.1586116	MS4A2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.7872340
1.2942396	NAPA	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.8510638
0.6835923	NFKBIA	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.2872340
0.8092696	PABPC1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.4148936
1.3775667	PELI1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.8617021
0.4810959	PLAU	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.1276596
0.9093989	PLXNC1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.5531915
0.9565624	PPBP	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.5957447
1.2898648	PPP3R1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.8404255
0.6138724	PSEN1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.2340426
0.4841938	PTPN18	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.1382979
0.6442788	QKI	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.2553191
0.5483505	RALGPS2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.1702128
0.2749511	RGS2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.0212766
0.8549743	SBNO2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.4574468
1.3819360	SELPLG	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.8723404
0.3111912	SEMA4D	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.0425532
1.0026812	SETX	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.6489362
0.6277688	SF3B1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.2446809
1.0292575	SH2B2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.6702128
0.7606755	SH3BGRL3	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.3829787
0.4294031	SMCHD1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.0851064
0.9633167	SPINK5	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.6063830
1.6740658	SULT1A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.9361702
0.3930779	TFEB	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.0638298
1.5923144	TFRC	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.9255319
0.9433092	TGFBI	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.5744681
0.5724803	THY1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.1808511
0.7471686	TIA1	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.3617021
0.8033264	TLR7	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.4042553
0.5304054	TNFRSF10C	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.1595745
1.7451465	TNFSF10	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.9574468
1.0225948	TNFSF4	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.6595745
0.8031226	ULBP2	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.3936170
1.0929130	VCAN	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.7659574
1.0435171	VPS13A	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.6808511
0.4280681	ZNF185	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.0744681
0.6032667	ZNF281	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.2021277
0.7352649	ZNF609	Exacer vs. followup (Moderate Persistent)	PLSDA	M+F	all	0.3510638
0.1396135	ABHD5	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.0106383
0.7988486	AHCTF1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.4893617
0.9629611	ARG2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.5957447
0.3828564	ATP11A	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.1276596
0.8129386	ATP8A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.5000000
0.7589839	C9orf78	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.4574468
0.5658763	CARM1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.2978723
1.1343572	CASP8	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.6808511
0.9687863	CD4	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.6063830
0.5373278	CD48	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.2765957
0.4153636	CD55	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.1489362
1.3508601	CD8A	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.7872340
1.2495845	CDH1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.7446809
1.6373619	CECR1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.9361702
0.4919764	CHP1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.2234043
0.9949460	CISH	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.6382979
0.9765410	CLEC4E	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.6170213
1.6237651	COPB1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.9255319
0.6527438	CREBBP	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.3829787
0.1897557	CTDSP2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.0212766
1.6692665	CTSA	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.9680851
1.2278565	CXCL10	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.7340426
0.2870357	CXCL2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.0744681
1.9121852	CXCL6	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	1.0000000
0.5108992	DAP	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.2446809
0.4934947	DESI1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.2340426
0.2259296	F13A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.0425532
0.5907349	FAM8A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.3297872
1.1839824	FOS	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.7127660
0.2305321	FOXJ1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.0531915
0.6358279	FPR1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.3723404
1.3552043	FPR2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.7978723
0.5939792	FUT7	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.3404255
0.3359563	GBE1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.1063830
1.0121174	GNAS	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.6489362
1.2552978	GNLY	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.7659574
1.8597532	IFI35	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.9893617
1.0908055	IFRD1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.6595745
0.8887007	IL15RA	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.5638298
0.0622729	IL1R1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.0000000
0.5354975	IL1R2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.2553191
1.6402085	IL26	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.9468085
0.9484873	IL32	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.5851064
0.7095413	ITGA2B	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.4255319
0.4630814	ITSN1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.1914894
1.2648564	JAM3	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.7765957
1.1010261	KIAA1551	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.6702128
1.5683017	KRT23	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.8936170
0.3102065	LCN2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.0957447
1.8189911	LCP1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.9787234
1.6532161	LILRB1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.9574468
0.4839587	LMBRD1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.2127660
1.2496831	LYST	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.7553191
0.6713329	MAP3K5	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.3936170
0.5367220	MAP3K8	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.2659574
0.7184775	MME	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.4361702
1.3696782	MS4A2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.8085106
1.5681780	NAPA	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.8829787
0.5840851	NFKBIA	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.3191489
1.4967716	PABPC1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.8723404
0.8705394	PELI1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.5531915
0.2168806	PLAU	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.0319149
1.4579771	PLXNC1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.8617021
0.9394627	PPBP	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.5744681
0.6184122	PPP3R1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.3510638
1.4233356	PSEN1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.8191489
0.8628199	PTPN18	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.5212766
1.1437896	QKI	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.6914894
0.7453109	RALGPS2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.4468085
0.2739491	RGS2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.0638298
0.7866759	SBNO2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.4787234
1.5888118	SELPLG	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.9148936
0.5639124	SEMA4D	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.2872340
1.4487128	SETX	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.8510638
0.8672363	SF3B1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.5319149
1.5688750	SH2B2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.9042553
0.8387953	SH3BGRL3	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.5106383
0.8683161	SMCHD1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.5425532
1.4486471	SPINK5	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.8404255
1.2168380	SULT1A1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.7234043
1.1455468	TFEB	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.7021277
0.4461446	TFRC	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.1702128
0.6214079	TGFBI	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.3617021
0.5731580	THY1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.3085106
0.3866741	TIA1	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.1382979
0.4349756	TLR7	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.1595745
0.7644404	TNFRSF10C	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.4680851
1.4457916	TNFSF10	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.8297872
0.6889863	TNFSF4	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.4042553
0.6954569	ULBP2	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.4148936
0.9925742	VCAN	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.6276596
0.3646689	VPS13A	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.1170213
0.3001418	ZNF185	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.0851064
0.4745299	ZNF281	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.2021277
0.4624202	ZNF609	Exacer vs. followup (Moderate Persistent)	PLSDA	M	all	0.1808511
0.5124642	ABHD5	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.2340426
1.1954733	AHCTF1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.6914894
1.3586989	ARG2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.8617021
0.9113406	ATP11A	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.4893617
1.3225016	ATP8A1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.8191489
1.2422778	C9orf78	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.7659574
0.9164864	CARM1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.5000000
0.4293502	CASP8	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.1914894
0.2677468	CD4	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.1063830
1.5733992	CD48	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.9574468
1.3264908	CD55	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.8297872
1.2012063	CD8A	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.7127660
0.2117935	CDH1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.0744681
1.1135317	CECR1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.6489362
0.4714383	CHP1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.2127660
1.4405875	CISH	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.9042553
1.7132021	CLEC4E	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.9893617
1.5494814	COPB1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.9468085
0.2004943	CREBBP	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.0638298
0.6405551	CTDSP2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.2978723
1.7007884	CTSA	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.9787234
1.1385226	CXCL10	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.6702128
0.7464985	CXCL2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.3404255
0.3733400	CXCL6	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.1595745
0.9520121	DAP	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.5319149
1.0008131	DESI1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.5531915
0.2153429	F13A1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.0851064
0.8596094	FAM8A1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.4468085
0.4961778	FOS	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.2234043
0.2709366	FOXJ1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.1170213
1.3468404	FPR1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.8510638
1.2411751	FPR2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.7553191
1.2004327	FUT7	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.7021277
0.0454819	GBE1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.0000000
1.2023492	GNAS	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.7234043
1.2823566	GNLY	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.7872340
1.3877940	IFI35	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.8723404
0.6289623	IFRD1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.2872340
0.7617012	IL15RA	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.3723404
0.8368780	IL1R1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.4255319
1.1057004	IL1R2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.6382979
0.7562368	IL26	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.3617021
0.0815110	IL32	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.0106383
0.8686432	ITGA2B	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.4574468
1.0164793	ITSN1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.5744681
0.7829783	JAM3	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.3936170
0.5450374	KIAA1551	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.2553191
1.0704684	KRT23	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.6063830
0.9061781	LCN2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.4787234
1.0489841	LCP1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.5957447
1.4659739	LILRB1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.9255319
1.4155443	LMBRD1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.8829787
0.2617321	LYST	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.0957447
0.6008090	MAP3K5	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.2765957
0.7647225	MAP3K8	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.3829787
1.0021588	MME	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.5638298
0.4556744	MS4A2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.2021277
1.9707302	NAPA	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	1.0000000
0.7542995	NFKBIA	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.3510638
1.4430928	PABPC1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.9148936
0.6518819	PELI1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.3191489
1.3191707	PLAU	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.8085106
1.1806643	PLXNC1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.6808511
0.1454084	PPBP	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.0212766
0.9379708	PPP3R1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.5212766
0.5321064	PSEN1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.2446809
0.5938977	PTPN18	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.2659574
0.8477099	QKI	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.4361702
0.8177827	RALGPS2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.4148936
0.4050841	RGS2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.1808511
1.6342169	SBNO2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.9680851
0.9624975	SELPLG	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.5425532
0.3154286	SEMA4D	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.1276596
1.0749971	SETX	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.6170213
1.4275942	SF3B1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.8936170
1.5413017	SH2B2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.9361702
1.0986191	SH3BGRL3	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.6276596
0.3615408	SMCHD1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.1489362
0.8156305	SPINK5	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.4042553
0.8844474	SULT1A1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.4680851
1.2344294	TFEB	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.7340426
1.2510662	TFRC	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.7765957
0.1558861	TGFBI	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.0319149
0.1976275	THY1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.0531915
1.1309605	TIA1	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.6595745
0.3871843	TLR7	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.1702128
1.3410333	TNFRSF10C	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.8404255
1.2898611	TNFSF10	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.7978723
0.9345289	TNFSF4	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.5106383
0.7417396	ULBP2	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.3297872
0.6496905	VCAN	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.3085106
0.1969074	VPS13A	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.0425532
1.0343398	ZNF185	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.5851064
1.2348253	ZNF281	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.7446809
0.3265706	ZNF609	Exacer vs. Quiet (Severe Persistent)	PLSDA	M	all	0.1382979
1.3484016	ABHD5	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.8510638
0.4478972	AHCTF1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.1382979
1.4218162	ARG2	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.9042553
0.7456570	ATP11A	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.3617021
1.2660754	ATP8A1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.7446809
1.5631292	C9orf78	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.9468085
1.0959739	CARM1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.6595745
1.0095342	CASP8	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.5957447
0.1400973	CD4	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.0319149
1.3057807	CD48	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.8297872
0.3049016	CD55	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.0744681
0.6834716	CD8A	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.3085106
1.4330091	CDH1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.9148936
1.3502096	CECR1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.8617021
0.6727582	CHP1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.2765957
2.0308699	CISH	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	1.0000000
1.4131070	CLEC4E	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.8936170
1.3446453	COPB1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.8404255
1.0877906	CREBBP	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.6489362
0.1386966	CTDSP2	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.0212766
1.7372205	CTSA	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.9787234
1.3046308	CXCL10	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.8191489
0.7667622	CXCL2	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.4148936
0.2328572	CXCL6	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.0425532
1.2838530	DAP	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.7978723
1.2708522	DESI1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.7659574
0.8802278	F13A1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.5000000
1.5105222	FAM8A1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.9255319
0.4971119	FOS	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.2021277
0.6539989	FOXJ1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.2659574
0.9281356	FPR1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.5319149
0.7092497	FPR2	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.3297872
0.4043475	FUT7	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.0957447
0.4765746	GBE1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.1808511
1.2680730	GNAS	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.7553191
0.4853963	GNLY	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.1914894
1.2834166	IFI35	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.7872340
0.4604357	IFRD1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.1595745
0.5055353	IL15RA	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.2234043
0.0348757	IL1R1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.0000000
0.3009575	IL1R2	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.0638298
0.5381023	IL26	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.2340426
0.9312434	IL32	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.5425532
0.6775143	ITGA2B	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.2872340
1.0657348	ITSN1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.6382979
0.4666038	JAM3	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.1702128
0.0823728	KIAA1551	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.0106383
0.9421387	KRT23	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.5744681
0.7238471	LCN2	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.3404255
0.7479778	LCP1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.3723404
1.7418101	LILRB1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.9893617
0.7593935	LMBRD1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.3936170
0.7361123	LYST	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.3510638
1.4120753	MAP3K5	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.8829787
0.4451246	MAP3K8	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.1276596
0.6038825	MME	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.2553191
1.3913620	MS4A2	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.8723404
1.6152880	NAPA	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.9574468
0.4568003	NFKBIA	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.1489362
1.1076400	PABPC1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.6702128
0.8534011	PELI1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.4787234
0.4202558	PLAU	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.1063830
0.7718249	PLXNC1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.4255319
0.8284946	PPBP	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.4680851
0.7502207	PPP3R1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.3829787
0.9118929	PSEN1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.5212766
1.1349047	PTPN18	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.6914894
0.9398062	QKI	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.5638298
0.7630066	RALGPS2	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.4042553
0.8572447	RGS2	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.4893617
1.2170012	SBNO2	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.7234043
1.0613995	SELPLG	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.6276596
0.4398813	SEMA4D	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.1170213
1.2713613	SETX	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.7765957
1.1529934	SF3B1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.7021277
1.3031287	SH2B2	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.8085106
1.2603972	SH3BGRL3	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.7340426
0.9335869	SMCHD1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.5531915
0.5018163	SPINK5	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.2127660
0.8093874	SULT1A1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.4361702
1.5433500	TFEB	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.9361702
1.6803851	TFRC	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.9680851
0.5663461	TGFBI	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.2446809
1.1216031	THY1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.6808511
0.8182276	TIA1	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.4468085
0.8246908	TLR7	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.4574468
0.7001777	TNFRSF10C	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.3191489
0.8830002	TNFSF10	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.5106383
1.0561088	TNFSF4	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.6063830
0.3708068	ULBP2	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.0851064
0.9890218	VCAN	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.5851064
0.6784745	VPS13A	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.2978723
1.1977665	ZNF185	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.7127660
0.2398762	ZNF281	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.0531915
1.0596474	ZNF609	Exacer vs. followup (Severe Persistent)	PLSDA	M	all	0.6170213
1.6483319	NAPA	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	1.0000000
1.2215143	PABPC1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.9615385
1.1876886	FOS	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.9230769
1.1420024	SULT1A1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.8846154
0.9684946	CD8A	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.8461538
0.9632819	KRT23	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.8076923
0.7299384	GNLY	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.7692308
0.5030140	AHCTF1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.7307692
0.4978819	CASP8	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.6923077
0.4406599	CD4	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.6538462
0.4390029	ATP8A1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.6153846
0.4190581	DAP	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.5769231
0.3631776	CLEC4E	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.5384615
0.3573472	PPP3R1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.5000000
0.3440702	FAM8A1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.4615385
0.3433325	NFKBIA	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.4230769
0.3324228	C9orf78	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.3846154
0.2918336	SF3B1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.3461538
0.2891447	RGS2	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.3076923
0.2602302	LMBRD1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.2692308
0.2584685	CARM1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.2307692
0.2528424	FUT7	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.1923077
0.2317915	F13A1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.1538462
0.2026021	SH3BGRL3	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.1153846
0.2005024	ABHD5	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.0769231
0.1731607	ZNF185	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.0384615
0.1521904	TGFBI	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC	0.0000000
3.5211971	NAPA	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	1.0000000
1.9769944	GNLY	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.9615385
1.8468110	LMBRD1	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.9230769
1.5826367	SF3B1	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.8846154
1.4829411	ATP8A1	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.8461538
1.2767308	CLEC4E	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.8076923
1.1282987	ZNF185	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.7692308
1.0385736	CD8A	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.7307692
0.9453193	KRT23	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.6923077
0.9406455	AHCTF1	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.6538462
0.9033477	DAP	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.6153846
0.8604204	CARM1	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.5769231
0.7525205	FAM8A1	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.5384615
0.7463590	PABPC1	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.5000000
0.7099340	ABHD5	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.4615385
0.7069263	SH3BGRL3	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.4230769
0.7028093	PPP3R1	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.3846154
0.6923057	RGS2	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.3461538
0.6480655	FOS	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.3076923
0.5356884	C9orf78	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.2692308
0.5278921	TGFBI	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.2307692
0.5160690	F13A1	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.1923077
0.4880163	SULT1A1	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.1538462
0.4851131	FUT7	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.1153846
0.4728528	CASP8	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.0769231
0.4359890	CD4	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.0384615
0.3875606	NFKBIA	Exacer vs. Quiet (Severe Persistent)	RF	M	UCSC	0.0000000
3.8906030	COPB1	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	1.0000000
3.4947075	FPR2	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.9642857
3.2816135	GNLY	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.9285714
2.3721268	ZNF609	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.8928571
2.2789170	IL1R2	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.8571429
2.2266144	GNAS	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.8214286
2.0770466	SULT1A1	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.7857143
1.9809235	NAPA	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.7500000
1.8513830	TGFBI	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.7142857
1.8018028	NFKBIA	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.6785714
1.7775901	CLEC4E	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.6428571
1.7597839	PTPN18	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.6071429
1.7129056	MME	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.5714286
1.7030109	TIA1	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.5357143
1.5855105	VCAN	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.5000000
1.4432953	SH3BGRL3	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.4642857
1.4420080	SEMA4D	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.4285714
1.3167387	PLXNC1	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.3928571
1.3078328	F13A1	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.3571429
1.3053930	CD8A	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.3214286
1.2992624	ATP8A1	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.2857143
1.2519965	QKI	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.2500000
1.2159475	SF3B1	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.2142857
1.1934201	MAP3K8	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.1785714
1.1901156	FAM8A1	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.1428571
1.1798317	PELI1	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.1071429
1.1434725	RGS2	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.0714286
1.1364117	VPS13A	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.0357143
1.0025358	ATP11A	Exacer vs. followup (Moderate Persistent)	RF	M+F	UCSC_isoforms	0.0000000
2.0359292	COPB1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	1.0000000
1.5738640	FPR2	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.9642857
1.4393023	NAPA	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.9285714
0.9382633	SULT1A1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.8928571
0.8308765	CD8A	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.8571429
0.7666487	PLXNC1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.8214286
0.6238035	GNLY	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.7857143
0.4868828	CLEC4E	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.7500000
0.4420603	ATP8A1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.7142857
0.4372391	PTPN18	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.6785714
0.3828086	QKI	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.6428571
0.3773260	ZNF609	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.6071429
0.3608587	FAM8A1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.5714286
0.3443923	NFKBIA	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.5357143
0.3095928	SF3B1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.5000000
0.2884452	IL1R2	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.4642857
0.2678763	GNAS	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.4285714
0.2485869	ATP11A	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.3928571
0.2458071	PELI1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.3571429
0.2428644	RGS2	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.3214286
0.2283755	SEMA4D	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.2857143
0.2246229	F13A1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.2500000
0.2217851	SH3BGRL3	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.2142857
0.2184514	VPS13A	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.1785714
0.2151287	TIA1	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.1428571
0.2113538	MME	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.1071429
0.1972939	VCAN	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.0714286
0.1783882	TGFBI	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.0357143
0.1420483	MAP3K8	Exacer vs. followup (Moderate Persistent)	RF	M	UCSC_isoforms	0.0000000
1.4332446	CTSA	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	1.0000000
1.2002262	PABPC1	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.9642857
1.1928139	KRT23	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.9285714
0.8886618	CD8A	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.8928571
0.8736077	KIAA1551	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.8571429
0.7509738	GNLY	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.8214286
0.6599718	RALGPS2	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.7857143
0.5009654	AHCTF1	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.7500000
0.4614926	ATP8A1	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.7142857
0.4549311	DAP	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.6785714
0.4505017	CISH	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.6428571
0.4046119	SF3B1	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.6071429
0.3930553	ZNF281	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.5714286
0.3873027	PPP3R1	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.5357143
0.3827889	RGS2	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.5000000
0.3765292	SMCHD1	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.4642857
0.3493112	C9orf78	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.4285714
0.3452193	FAM8A1	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.3928571
0.3434742	DESI1	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.3571429
0.3400410	CLEC4E	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.3214286
0.2579773	F13A1	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.2857143
0.2518637	CHP1	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.2500000
0.2478159	ITSN1	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.2142857
0.2437364	CARM1	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.1785714
0.1806314	ZNF185	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.1428571
0.1787140	TGFBI	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.1071429
0.1776296	SH3BGRL3	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.0714286
0.1724769	CTDSP2	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.0357143
0.1566044	GBE1	Exacer vs. followup (Moderate Persistent)	RF	M	Ensembl	0.0000000
2.5434442	CTSA	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	1.0000000
2.0284684	GNLY	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.9642857
1.6398851	SF3B1	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.9285714
1.5336018	ATP8A1	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.8928571
1.4004773	ITSN1	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.8571429
1.3558617	CLEC4E	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.8214286
1.2724168	CISH	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.7857143
0.9195698	CD8A	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.7500000
0.8646489	ZNF185	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.7142857
0.8567672	AHCTF1	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.6785714
0.8557052	ZNF281	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.6428571
0.8523397	KRT23	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.6071429
0.7764252	DAP	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.5714286
0.7734722	KIAA1551	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.5357143
0.7438804	CARM1	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.5000000
0.7129546	RALGPS2	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.4642857
0.7015388	DESI1	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.4285714
0.6926284	PPP3R1	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.3928571
0.6894176	PABPC1	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.3571429
0.6547623	FAM8A1	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.3214286
0.6393946	SH3BGRL3	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.2857143
0.5869285	SMCHD1	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.2500000
0.5677264	RGS2	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.2142857
0.5174339	C9orf78	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.1785714
0.4930798	CTDSP2	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.1428571
0.4677419	F13A1	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.1071429
0.4630648	TGFBI	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.0714286
0.3962731	CHP1	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.0357143
0.3223546	GBE1	Exacer vs. Quiet (Severe Persistent)	RF	M	Ensembl	0.0000000
2.9675732	CISH	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	1.0000000
1.4208627	C9orf78	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.9642857
1.2071977	CARM1	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.9285714
0.8501989	FAM8A1	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.8928571
0.7987276	CTSA	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.8571429
0.7806397	ATP8A1	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.8214286
0.7575974	DAP	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.7857143
0.5618383	SF3B1	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.7500000
0.5566718	ITSN1	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.7142857
0.5405840	CHP1	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.6785714
0.5380819	CLEC4E	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.6428571
0.5307837	CD8A	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.6071429
0.4996230	PPP3R1	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.5714286
0.4860007	GNLY	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.5357143
0.4743808	TGFBI	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.5000000
0.4171533	KRT23	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.4642857
0.3538965	SMCHD1	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.4285714
0.3461305	KIAA1551	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.3928571
0.3254522	SH3BGRL3	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.3571429
0.3239945	RALGPS2	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.3214286
0.2994798	DESI1	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.2857143
0.2834036	AHCTF1	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.2500000
0.2703298	RGS2	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.2142857
0.2533589	ZNF281	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.1785714
0.2471389	CTDSP2	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.1428571
0.2451860	PABPC1	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.1071429
0.2227164	GBE1	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.0714286
0.2071250	ZNF185	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.0357143
0.1971144	F13A1	Exacer vs. followup (Severe Persistent)	RF	M	Ensembl	0.0000000
2.9792244	FPR2	Exacer vs. followup (Moderate Persistent)	RF	M	Trinity	1.0000000
2.5830493	CECR1	Exacer vs. followup (Moderate Persistent)	RF	M	Trinity	0.8888889
2.0992622	LYST	Exacer vs. followup (Moderate Persistent)	RF	M	Trinity	0.7777778
1.5831344	FPR1	Exacer vs. followup (Moderate Persistent)	RF	M	Trinity	0.6666667
1.1912095	SETX	Exacer vs. followup (Moderate Persistent)	RF	M	Trinity	0.5555556
1.0114469	QKI	Exacer vs. followup (Moderate Persistent)	RF	M	Trinity	0.4444444
0.8956291	CASP8	Exacer vs. followup (Moderate Persistent)	RF	M	Trinity	0.3333333
0.6256590	IFRD1	Exacer vs. followup (Moderate Persistent)	RF	M	Trinity	0.2222222
0.5673338	TNFRSF10C	Exacer vs. followup (Moderate Persistent)	RF	M	Trinity	0.1111111
0.5452258	SF3B1	Exacer vs. followup (Moderate Persistent)	RF	M	Trinity	0.0000000
4.6763890	IFI35	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	1.0000000
3.0343676	IL32	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.9729730
2.9012682	TFRC	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.9459459
2.7436535	LCP1	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.9189189
2.7233895	TNFSF10	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.8918919
1.7324530	SELPLG	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.8648649
1.5690020	IL1R1	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.8378378
1.5678528	FOXJ1	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.8108108
1.5241533	JAM3	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.7837838
1.4176183	F13A1	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.7567568
1.3071295	CDH1	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.7297297
1.2874249	CD55	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.7027027
1.2444854	SPINK5	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.6756757
1.2334565	CXCL2	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.6486486
1.2206217	MS4A2	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.6216216
1.2197747	TNFSF4	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.5945946
1.2140558	LCN2	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.5675676
1.1783080	MAP3K5	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.5405405
1.1432048	ULBP2	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.5135135
1.1402292	PSEN1	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.4864865
1.1343725	FUT7	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.4594595
1.1073369	ITGA2B	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.4324324
1.0360764	SH2B2	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.4054054
1.0079184	CXCL6	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.3783784
0.9811892	CREBBP	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.3513514
0.9769498	LILRB1	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.3243243
0.9679311	PPBP	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.2972973
0.9353799	CXCL10	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.2702703
0.9196267	IL26	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.2432432
0.9125187	FOS	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.2162162
0.8610929	SBNO2	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.1891892
0.8031919	THY1	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.1621622
0.7916470	TLR7	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.1351351
0.7816229	CD48	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.1081081
0.7374204	PLAU	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.0810811
0.7320900	TFEB	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.0540541
0.6529100	ARG2	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.0270270
0.6363121	IL15RA	Exacer vs. followup (Moderate Persistent)	RF	M+F	panCancer	0.0000000
5.1761319	LCN2	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	1.0000000
3.1767779	SBNO2	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.9729730
3.1635956	TFRC	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.9459459
3.1211546	LILRB1	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.9189189
2.5560346	ARG2	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.8918919
2.4590297	TLR7	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.8648649
1.7287213	CXCL10	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.8378378
1.6487809	FOXJ1	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.8108108
1.5450024	THY1	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.7837838
1.4698245	PPBP	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.7567568
1.3898354	CREBBP	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.7297297
1.3317471	FOS	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.7027027
1.3175328	F13A1	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.6756757
1.3073323	IL1R1	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.6486486
1.2907947	SH2B2	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.6216216
1.2014450	SPINK5	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.5945946
1.1888926	TNFSF4	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.5675676
1.1878343	LCP1	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.5405405
1.1836741	FUT7	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.5135135
1.1732938	MAP3K5	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.4864865
1.0951154	CD48	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.4594595
1.0544187	TNFSF10	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.4324324
1.0348299	IL32	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.4054054
1.0119744	IFI35	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.3783784
1.0054395	ULBP2	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.3513514
0.9860552	PLAU	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.3243243
0.9623855	CXCL2	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.2972973
0.9348970	CXCL6	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.2702703
0.9028410	SELPLG	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.2432432
0.8910652	CD55	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.2162162
0.8892866	CDH1	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.1891892
0.8851047	IL15RA	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.1621622
0.8754585	ITGA2B	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.1351351
0.8650684	IL26	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.1081081
0.8599673	TFEB	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.0810811
0.8467405	JAM3	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.0540541
0.8118223	PSEN1	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.0270270
0.7930909	MS4A2	Exacer vs. followup (Severe Persistent)	RF	M+F	panCancer	0.0000000
1.5064110	LCP1	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	1.0000000
1.3571805	IFI35	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.9729730
0.8552221	SH2B2	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.9459459
0.8366085	SELPLG	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.9189189
0.8256620	TFEB	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.8918919
0.7764311	FOS	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.8648649
0.7353732	IL26	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.8378378
0.6805554	CXCL10	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.8108108
0.6612078	SPINK5	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.7837838
0.5576226	PSEN1	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.7567568
0.4872952	CXCL6	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.7297297
0.3832219	CXCL2	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.7027027
0.3576760	LILRB1	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.6756757
0.3367590	PPBP	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.6486486
0.3259764	CDH1	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.6216216
0.2869146	MS4A2	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.5945946
0.2632695	TNFSF10	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.5675676
0.2530777	IL32	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.5405405
0.2398407	THY1	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.5135135
0.2257727	JAM3	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.4864865
0.2210258	CD48	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.4594595
0.2118259	TLR7	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.4324324
0.2027532	MAP3K5	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.4054054
0.1711214	F13A1	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.3783784
0.1587560	ARG2	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.3513514
0.1585486	FOXJ1	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.3243243
0.1578662	IL15RA	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.2972973
0.1564844	CD55	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.2702703
0.1395892	FUT7	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.2432432
0.1382282	TFRC	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.2162162
0.1332447	CREBBP	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.1891892
0.1320836	ITGA2B	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.1621622
0.1300441	IL1R1	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.1351351
0.1267262	SBNO2	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.1081081
0.1177810	ULBP2	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.0810811
0.1166618	PLAU	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.0540541
0.0982033	LCN2	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.0270270
0.0924459	TNFSF4	Exacer vs. followup (Moderate Persistent)	RF	M	panCancer	0.0000000
2.4992493	IFI35	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	1.0000000
1.5590806	COPB1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.9893617
1.5321412	TFRC	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.9787234
1.5313017	TNFSF10	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.9680851
1.5192547	CTDSP2	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.9574468
1.4282795	IL32	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.9468085
1.4018036	CECR1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.9361702
1.2705644	FPR2	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.9255319
1.2496324	LCP1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.9148936
1.2092522	GNLY	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.9042553
1.0925521	PPP3R1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.8936170
0.9585687	CTSA	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.8829787
0.8115574	SULT1A1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.8723404
0.7841895	FOXJ1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.8617021
0.7657442	RALGPS2	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.8510638
0.7204773	SELPLG	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.8404255
0.7176659	ZNF609	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.8297872
0.6892771	JAM3	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.8191489
0.6732067	TGFBI	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.8085106
0.6247116	FPR1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.7978723
0.5984826	VCAN	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.7872340
0.5894501	PABPC1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.7765957
0.5868274	IL1R2	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.7659574
0.5721608	IL1R1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.7553191
0.5693180	LCN2	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.7446809
0.5640821	CARM1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.7340426
0.5608685	LYST	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.7234043
0.5513177	MS4A2	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.7127660
0.5481626	NAPA	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.7021277
0.5435996	TNFSF4	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.6914894
0.5394723	SEMA4D	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.6808511
0.5366075	CD55	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.6702128
0.5304477	PTPN18	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.6595745
0.5303258	CDH1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.6489362
0.5237753	GNAS	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.6382979
0.5223673	FUT7	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.6276596
0.5208003	GBE1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.6170213
0.5207901	CLEC4E	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.6063830
0.5093770	TIA1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.5957447
0.5012580	SPINK5	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.5851064
0.4994948	PSEN1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.5744681
0.4972576	ULBP2	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.5638298
0.4809378	MME	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.5531915
0.4587081	NFKBIA	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.5425532
0.4556900	CD4	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.5319149
0.4477971	CXCL2	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.5212766
0.4450328	CASP8	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.5106383
0.4445303	MAP3K5	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.5000000
0.4395425	F13A1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.4893617
0.4216989	SF3B1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.4787234
0.4057397	C9orf78	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.4680851
0.4036545	CD8A	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.4574468
0.4023768	KRT23	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.4468085
0.4002584	IFRD1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.4361702
0.3896357	FOS	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.4255319
0.3825598	QKI	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.4148936
0.3824130	SH2B2	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.4042553
0.3749221	PPBP	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.3936170
0.3710450	CISH	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.3829787
0.3653304	CXCL10	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.3723404
0.3649257	LMBRD1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.3617021
0.3580858	SH3BGRL3	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.3510638
0.3531470	CXCL6	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.3404255
0.3464034	PLXNC1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.3297872
0.3450587	RGS2	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.3191489
0.3429578	ATP8A1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.3085106
0.3423992	CD48	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.2978723
0.3422331	CREBBP	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.2872340
0.3390372	ZNF281	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.2765957
0.3388144	IL26	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.2659574
0.3379404	ITGA2B	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.2553191
0.3314107	KIAA1551	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.2446809
0.3293782	ITSN1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.2340426
0.3273829	THY1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.2234043
0.3241534	CHP1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.2127660
0.3181441	LILRB1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.2021277
0.3180674	VPS13A	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.1914894
0.3167278	PELI1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.1808511
0.3148383	TNFRSF10C	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.1702128
0.3139736	AHCTF1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.1595745
0.3114090	SMCHD1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.1489362
0.3109895	ABHD5	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.1382979
0.3071238	MAP3K8	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.1276596
0.3060691	SETX	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.1170213
0.3055129	DAP	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.1063830
0.3043818	SBNO2	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.0957447
0.3007054	TLR7	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.0851064
0.2994434	FAM8A1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.0744681
0.2989667	ZNF185	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.0638298
0.2985182	PLAU	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.0531915
0.2773992	IL15RA	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.0425532
0.2701149	DESI1	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.0319149
0.2532216	TFEB	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.0212766
0.2477506	ATP11A	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.0106383
0.2332065	ARG2	Exacer vs. followup (Moderate Persistent)	RF	M+F	all	0.0000000
0.8432418	COPB1	Exacer vs. followup (Moderate Persistent)	RF	M	all	1.0000000
0.6806352	LCP1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.9893617
0.6618034	IFI35	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.9787234
0.5983545	FPR2	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.9680851
0.5152984	NAPA	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.9574468
0.4409555	CTSA	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.9468085
0.4404084	SH2B2	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.9361702
0.4028379	SELPLG	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.9255319
0.3907419	CECR1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.9148936
0.3687625	TFEB	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.9042553
0.3508908	CXCL10	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.8936170
0.3437976	PABPC1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.8829787
0.3322482	FOS	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.8723404
0.3222834	LYST	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.8617021
0.3146154	IL26	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.8510638
0.3082532	SPINK5	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.8404255
0.3014327	CD8A	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.8297872
0.2836917	SULT1A1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.8191489
0.2714251	KRT23	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.8085106
0.2683609	PLXNC1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.7978723
0.2581258	KIAA1551	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.7872340
0.2511248	PSEN1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.7765957
0.2120294	CXCL6	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.7659574
0.2043998	FPR1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.7553191
0.1994261	SETX	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.7446809
0.1749906	GNLY	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.7340426
0.1680009	RALGPS2	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.7234043
0.1554087	LILRB1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.7127660
0.1547540	CDH1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.7021277
0.1479730	PPBP	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.6914894
0.1465464	CXCL2	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.6808511
0.1325185	AHCTF1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.6702128
0.1307489	CD4	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.6595745
0.1243429	PTPN18	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.6489362
0.1217411	CASP8	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.6382979
0.1141595	CLEC4E	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.6276596
0.1132913	QKI	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.6170213
0.1120503	IL32	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.6063830
0.1092749	CISH	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.5957447
0.1086943	ZNF281	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.5851064
0.1070915	TNFSF10	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.5744681
0.1058054	MS4A2	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.5638298
0.1044493	ATP8A1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.5531915
0.0996354	RGS2	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.5425532
0.0958575	ZNF609	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.5319149
0.0929231	PPP3R1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.5212766
0.0920698	CD48	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.5106383
0.0905601	THY1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.5000000
0.0904015	DAP	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.4893617
0.0866161	TNFRSF10C	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.4787234
0.0850706	NFKBIA	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.4680851
0.0842794	IFRD1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.4574468
0.0824751	JAM3	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.4468085
0.0810823	TLR7	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.4361702
0.0802064	FAM8A1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.4255319
0.0796094	SF3B1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.4148936
0.0744203	MAP3K5	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.4042553
0.0706146	IL1R1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.3936170
0.0682518	ITSN1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.3829787
0.0678172	SMCHD1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.3723404
0.0657266	DESI1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.3617021
0.0653213	TFRC	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.3510638
0.0648434	VPS13A	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.3404255
0.0647311	ARG2	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.3297872
0.0644586	SEMA4D	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.3191489
0.0624633	IL15RA	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.3085106
0.0624112	IL1R2	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.2978723
0.0596049	GNAS	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.2872340
0.0559308	CD55	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.2765957
0.0557631	FOXJ1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.2659574
0.0557504	ULBP2	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.2553191
0.0552915	C9orf78	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.2446809
0.0542578	TIA1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.2340426
0.0536453	F13A1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.2234043
0.0534446	FUT7	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.2127660
0.0531091	ATP11A	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.2021277
0.0528648	CARM1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.1914894
0.0526577	MME	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.1808511
0.0526434	CHP1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.1702128
0.0490216	SH3BGRL3	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.1595745
0.0489080	ABHD5	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.1489362
0.0483535	PELI1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.1382979
0.0476859	LMBRD1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.1276596
0.0439287	VCAN	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.1170213
0.0435539	CREBBP	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.1063830
0.0433843	ITGA2B	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.0957447
0.0430531	TGFBI	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.0851064
0.0427473	MAP3K8	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.0744681
0.0426412	ZNF185	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.0638298
0.0407514	GBE1	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.0531915
0.0389356	SBNO2	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.0425532
0.0349038	TNFSF4	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.0319149
0.0335562	LCN2	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.0212766
0.0326096	CTDSP2	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.0106383
0.0289418	PLAU	Exacer vs. followup (Moderate Persistent)	RF	M	all	0.0000000
1.5995743	NAPA	Exacer vs. Quiet (Severe Persistent)	RF	M	all	1.0000000
1.0660948	CTSA	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.9893617
0.7149678	PLAU	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.9787234
0.7006343	LILRB1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.9680851
0.6754472	GNLY	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.9574468
0.6545321	LMBRD1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.9468085
0.6226345	CD55	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.9361702
0.5978595	TNFSF10	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.9255319
0.5902124	ARG2	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.9148936
0.5683082	SBNO2	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.9042553
0.5590501	SF3B1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.8936170
0.5567732	ITSN1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.8829787
0.5517946	CLEC4E	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.8723404
0.5270537	IFI35	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.8617021
0.5224446	ATP8A1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.8510638
0.5010799	CREBBP	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.8404255
0.4635815	TFRC	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.8297872
0.4313360	CXCL10	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.8191489
0.4262272	CISH	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.8085106
0.4112705	CD48	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.7978723
0.4005557	TFEB	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.7872340
0.3888777	TNFRSF10C	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.7765957
0.3818647	ZNF185	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.7659574
0.3601640	IL1R1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.7553191
0.3093180	TLR7	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.7446809
0.3065468	CD8A	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.7340426
0.3049673	ZNF281	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.7234043
0.2973143	KIAA1551	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.7127660
0.2893135	LCP1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.7021277
0.2791582	DAP	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.6914894
0.2788271	LCN2	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.6808511
0.2685365	KRT23	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.6702128
0.2637961	FOXJ1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.6595745
0.2633822	IL1R2	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.6489362
0.2561331	DESI1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.6382979
0.2554552	FAM8A1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.6276596
0.2519666	QKI	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.6170213
0.2515763	FPR2	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.6063830
0.2458430	ATP11A	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.5957447
0.2442738	CARM1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.5851064
0.2367909	SPINK5	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.5744681
0.2355991	TIA1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.5638298
0.2304390	PPP3R1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.5531915
0.2302586	CECR1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.5425532
0.2170319	RGS2	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.5319149
0.2168446	GNAS	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.5212766
0.2161923	AHCTF1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.5106383
0.2139182	PABPC1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.5000000
0.2136967	RALGPS2	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.4893617
0.2131007	SH3BGRL3	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.4787234
0.2042368	SH2B2	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.4680851
0.1996121	TNFSF4	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.4574468
0.1985879	IFRD1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.4468085
0.1888790	VCAN	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.4361702
0.1871448	IL26	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.4255319
0.1866361	FOS	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.4148936
0.1826209	MME	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.4042553
0.1798010	ABHD5	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.3936170
0.1775425	THY1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.3829787
0.1758190	MS4A2	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.3723404
0.1705299	FPR1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.3617021
0.1656096	ITGA2B	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.3510638
0.1649987	SMCHD1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.3404255
0.1646773	MAP3K8	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.3297872
0.1578163	SETX	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.3191489
0.1559633	SELPLG	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.3085106
0.1542973	PPBP	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.2978723
0.1460887	F13A1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.2872340
0.1431690	PSEN1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.2765957
0.1381847	CDH1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.2659574
0.1331874	CTDSP2	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.2553191
0.1324199	JAM3	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.2446809
0.1309536	CASP8	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.2340426
0.1277235	C9orf78	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.2234043
0.1268394	VPS13A	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.2127660
0.1263002	PLXNC1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.2021277
0.1251611	FUT7	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.1914894
0.1251352	IL15RA	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.1808511
0.1219146	CXCL2	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.1702128
0.1204470	PTPN18	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.1595745
0.1190565	MAP3K5	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.1489362
0.1183569	CXCL6	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.1382979
0.1176376	COPB1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.1276596
0.1143271	SEMA4D	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.1170213
0.1128748	CHP1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.1063830
0.1125037	ULBP2	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.0957447
0.1115709	TGFBI	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.0851064
0.1112852	SULT1A1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.0744681
0.1105531	PELI1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.0638298
0.1094487	ZNF609	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.0531915
0.1030929	LYST	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.0425532
0.1010073	CD4	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.0319149
0.0990358	IL32	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.0212766
0.0974917	GBE1	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.0106383
0.0940564	NFKBIA	Exacer vs. Quiet (Severe Persistent)	RF	M	all	0.0000000
1.4034011	CISH	Exacer vs. followup (Severe Persistent)	RF	M	all	1.0000000
0.9060675	LILRB1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.9893617
0.6747551	NAPA	Exacer vs. followup (Severe Persistent)	RF	M	all	0.9787234
0.5399177	C9orf78	Exacer vs. followup (Severe Persistent)	RF	M	all	0.9680851
0.4784575	CD48	Exacer vs. followup (Severe Persistent)	RF	M	all	0.9574468
0.4463557	CARM1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.9468085
0.3990510	TFRC	Exacer vs. followup (Severe Persistent)	RF	M	all	0.9361702
0.3870766	TNFRSF10C	Exacer vs. followup (Severe Persistent)	RF	M	all	0.9255319
0.3584940	SETX	Exacer vs. followup (Severe Persistent)	RF	M	all	0.9148936
0.3526188	SBNO2	Exacer vs. followup (Severe Persistent)	RF	M	all	0.9042553
0.3468955	CECR1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.8936170
0.3404579	ARG2	Exacer vs. followup (Severe Persistent)	RF	M	all	0.8829787
0.3359806	FAM8A1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.8723404
0.3126896	DAP	Exacer vs. followup (Severe Persistent)	RF	M	all	0.8617021
0.2868544	IFI35	Exacer vs. followup (Severe Persistent)	RF	M	all	0.8510638
0.2724368	ATP8A1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.8404255
0.2637813	CTSA	Exacer vs. followup (Severe Persistent)	RF	M	all	0.8297872
0.2619913	TNFSF4	Exacer vs. followup (Severe Persistent)	RF	M	all	0.8191489
0.2413308	SELPLG	Exacer vs. followup (Severe Persistent)	RF	M	all	0.8085106
0.2396137	PSEN1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.7978723
0.2284318	SF3B1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.7872340
0.2247025	FOS	Exacer vs. followup (Severe Persistent)	RF	M	all	0.7765957
0.2222947	IL32	Exacer vs. followup (Severe Persistent)	RF	M	all	0.7659574
0.2033828	CLEC4E	Exacer vs. followup (Severe Persistent)	RF	M	all	0.7553191
0.1986217	ABHD5	Exacer vs. followup (Severe Persistent)	RF	M	all	0.7446809
0.1905577	CHP1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.7340426
0.1902909	ITSN1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.7234043
0.1840148	CXCL2	Exacer vs. followup (Severe Persistent)	RF	M	all	0.7127660
0.1798963	LMBRD1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.7021277
0.1774282	TFEB	Exacer vs. followup (Severe Persistent)	RF	M	all	0.6914894
0.1715135	PPP3R1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.6808511
0.1690791	SPINK5	Exacer vs. followup (Severe Persistent)	RF	M	all	0.6702128
0.1647629	PELI1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.6595745
0.1639535	MME	Exacer vs. followup (Severe Persistent)	RF	M	all	0.6489362
0.1586859	CREBBP	Exacer vs. followup (Severe Persistent)	RF	M	all	0.6382979
0.1549825	TGFBI	Exacer vs. followup (Severe Persistent)	RF	M	all	0.6276596
0.1548415	PLAU	Exacer vs. followup (Severe Persistent)	RF	M	all	0.6170213
0.1532444	TLR7	Exacer vs. followup (Severe Persistent)	RF	M	all	0.6063830
0.1531044	LCN2	Exacer vs. followup (Severe Persistent)	RF	M	all	0.5957447
0.1505563	GNAS	Exacer vs. followup (Severe Persistent)	RF	M	all	0.5851064
0.1499424	VCAN	Exacer vs. followup (Severe Persistent)	RF	M	all	0.5744681
0.1489139	CD8A	Exacer vs. followup (Severe Persistent)	RF	M	all	0.5638298
0.1411545	CDH1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.5531915
0.1401908	MS4A2	Exacer vs. followup (Severe Persistent)	RF	M	all	0.5425532
0.1355880	SMCHD1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.5319149
0.1335883	TIA1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.5212766
0.1333384	LYST	Exacer vs. followup (Severe Persistent)	RF	M	all	0.5106383
0.1299377	ATP11A	Exacer vs. followup (Severe Persistent)	RF	M	all	0.5000000
0.1254962	ZNF609	Exacer vs. followup (Severe Persistent)	RF	M	all	0.4893617
0.1247461	GNLY	Exacer vs. followup (Severe Persistent)	RF	M	all	0.4787234
0.1247456	FOXJ1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.4680851
0.1240788	FUT7	Exacer vs. followup (Severe Persistent)	RF	M	all	0.4574468
0.1225051	MAP3K8	Exacer vs. followup (Severe Persistent)	RF	M	all	0.4468085
0.1221927	IL15RA	Exacer vs. followup (Severe Persistent)	RF	M	all	0.4361702
0.1197468	PLXNC1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.4255319
0.1156396	QKI	Exacer vs. followup (Severe Persistent)	RF	M	all	0.4148936
0.1108925	LCP1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.4042553
0.1107846	KRT23	Exacer vs. followup (Severe Persistent)	RF	M	all	0.3936170
0.1085751	FPR1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.3829787
0.1081747	FPR2	Exacer vs. followup (Severe Persistent)	RF	M	all	0.3723404
0.1065578	VPS13A	Exacer vs. followup (Severe Persistent)	RF	M	all	0.3617021
0.1061351	SULT1A1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.3510638
0.1038340	CXCL10	Exacer vs. followup (Severe Persistent)	RF	M	all	0.3404255
0.1023103	TNFSF10	Exacer vs. followup (Severe Persistent)	RF	M	all	0.3297872
0.0991108	KIAA1551	Exacer vs. followup (Severe Persistent)	RF	M	all	0.3191489
0.0969852	CD4	Exacer vs. followup (Severe Persistent)	RF	M	all	0.3085106
0.0956706	DESI1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.2978723
0.0950325	IFRD1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.2872340
0.0933520	AHCTF1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.2765957
0.0902364	RALGPS2	Exacer vs. followup (Severe Persistent)	RF	M	all	0.2659574
0.0890534	SH3BGRL3	Exacer vs. followup (Severe Persistent)	RF	M	all	0.2553191
0.0850262	RGS2	Exacer vs. followup (Severe Persistent)	RF	M	all	0.2446809
0.0846507	CASP8	Exacer vs. followup (Severe Persistent)	RF	M	all	0.2340426
0.0824195	CD55	Exacer vs. followup (Severe Persistent)	RF	M	all	0.2234043
0.0817161	CTDSP2	Exacer vs. followup (Severe Persistent)	RF	M	all	0.2127660
0.0807123	PTPN18	Exacer vs. followup (Severe Persistent)	RF	M	all	0.2021277
0.0798204	CXCL6	Exacer vs. followup (Severe Persistent)	RF	M	all	0.1914894
0.0798027	MAP3K5	Exacer vs. followup (Severe Persistent)	RF	M	all	0.1808511
0.0787080	NFKBIA	Exacer vs. followup (Severe Persistent)	RF	M	all	0.1702128
0.0770730	THY1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.1595745
0.0759150	PABPC1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.1489362
0.0743729	COPB1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.1382979
0.0713779	JAM3	Exacer vs. followup (Severe Persistent)	RF	M	all	0.1276596
0.0697145	GBE1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.1170213
0.0696900	IL1R1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.1063830
0.0622675	SH2B2	Exacer vs. followup (Severe Persistent)	RF	M	all	0.0957447
0.0590771	F13A1	Exacer vs. followup (Severe Persistent)	RF	M	all	0.0851064
0.0572345	PPBP	Exacer vs. followup (Severe Persistent)	RF	M	all	0.0744681
0.0562168	ZNF185	Exacer vs. followup (Severe Persistent)	RF	M	all	0.0638298
0.0547922	ZNF281	Exacer vs. followup (Severe Persistent)	RF	M	all	0.0531915
0.0502393	IL1R2	Exacer vs. followup (Severe Persistent)	RF	M	all	0.0425532
0.0490545	ULBP2	Exacer vs. followup (Severe Persistent)	RF	M	all	0.0319149
0.0480472	SEMA4D	Exacer vs. followup (Severe Persistent)	RF	M	all	0.0212766
0.0442305	ITGA2B	Exacer vs. followup (Severe Persistent)	RF	M	all	0.0106383
0.0420836	IL26	Exacer vs. followup (Severe Persistent)	RF	M	all	0.0000000

Asthma severity

Train PLS-DA models (severity)

# all_sev <- lapply(names(latephase_biomarkers), function(i){
#   res <- lar_plsda(eset_list = esetList, pheno_list = phenoDataList, gse_list = select_gse,
#                      biomarkers = latephase_biomarkers[[i]])
#   list(feat = do.call(rbind, res$feat) %>% mutate(panel = i),
#        df = do.call(rbind, res$df) %>% mutate(panel = i))
# }) %>%
#   zip_nPure()
# pheno = lapply(phenoDataList, function(i){subset(i, sex == "F")})
# f_sev <- lapply(names(latephase_biomarkers), function(i){
#   res <- lar_plsda(eset_list = esetList, pheno_list = pheno, gse_list = select_gse,
#                      biomarkers = latephase_biomarkers[[i]])
#   list(feat = do.call(rbind, res$feat) %>% mutate(panel = i),
#        df = do.call(rbind, res$df) %>% mutate(panel = i))
# }) %>%
#   zip_nPure()
# pheno = lapply(phenoDataList, function(i){subset(i, sex == "M")})
# m_sev <- lapply(names(latephase_biomarkers), function(i){
#   res <- lar_plsda(eset_list = esetList, pheno_list = pheno, gse_list = select_gse,
#                      biomarkers = latephase_biomarkers[[i]])
#   list(feat = do.call(rbind, res$feat) %>% mutate(panel = i),
#        df = do.call(rbind, res$df) %>% mutate(panel = i))
# }) %>%
#   zip_nPure()
# 
# ## perf
# sev_plsda_df <- rbind(do.call(rbind, all_sev$df) %>% mutate(sex="M+F"),
#       do.call(rbind, f_sev$df) %>% mutate(sex="F"),
#       do.call(rbind, m_sev$df) %>% mutate(sex="M"))
# sev_plsda_df$sampletype[sev_plsda_df$sampletype == "balf"] <- "BALF"
# 
# ## feature importance
# sev_plsda_feat <- rbind(do.call(rbind, all_sev$feat) %>% mutate(sex="M+F"),
#       do.call(rbind, f_sev$feat) %>% mutate(sex="F"),
#       do.call(rbind, m_sev$feat) %>% mutate(sex="M"))
# sev_plsda_feat$sampletype[sev_plsda_feat$sampletype == "balf"] <- "BALF"
# sev_plsda <- list(feat = sev_plsda_feat, df = sev_plsda_df)
# 
# saveRDS(sev_plsda, here("results", "sev_plsda.rds"))

Train RF models (severity)

# all_sev <- lapply(names(latephase_biomarkers), function(i){
#   res <- lar_rf(eset_list = esetList, pheno_list = phenoDataList, gse_list = select_gse,
#                      biomarkers = latephase_biomarkers[[i]], workers = 8)
#   list(feat = do.call(rbind, res$feat) %>% mutate(panel = i),
#        df = do.call(rbind, res$df) %>% mutate(panel = i))
# }) %>%
#   zip_nPure()
# pheno = lapply(phenoDataList, function(i){subset(i, sex == "F")})
# f_sev <- lapply(names(latephase_biomarkers), function(i){
#   res <- lar_rf(eset_list = esetList, pheno_list = pheno, gse_list = select_gse,
#                      biomarkers = latephase_biomarkers[[i]], workers = 8)
#   list(feat = do.call(rbind, res$feat) %>% mutate(panel = i),
#        df = do.call(rbind, res$df) %>% mutate(panel = i))
# }) %>%
#   zip_nPure()
# pheno = lapply(phenoDataList, function(i){subset(i, sex == "M")})
# m_sev <- lapply(names(latephase_biomarkers), function(i){
#   res <- lar_rf(eset_list = esetList, pheno_list = pheno, gse_list = select_gse,
#                      biomarkers = latephase_biomarkers[[i]], workers = 8)
#   list(feat = do.call(rbind, res$feat) %>% mutate(panel = i),
#        df = do.call(rbind, res$df) %>% mutate(panel = i))
# }) %>%
#   zip_nPure()
# 
# ## perf
# sev_rf_df <- rbind(do.call(rbind, all_sev$df) %>% mutate(sex="M+F"),
#       do.call(rbind, f_sev$df) %>% mutate(sex="F"),
#       do.call(rbind, m_sev$df) %>% mutate(sex="M"))
# sev_rf_df$sampletype[sev_rf_df$sampletype == "balf"] <- "BALF"
# 
# ## feature importance
# sev_rf_feat <- rbind(do.call(rbind, all_sev$feat) %>% mutate(sex="M+F"),
#       do.call(rbind, f_sev$feat) %>% mutate(sex="F"),
#       do.call(rbind, m_sev$feat) %>% mutate(sex="M"))
# sev_rf_feat$sampletype[sev_rf_feat$sampletype == "balf"] <- "BALF"
# sev_rf <- list(feat = sev_rf_feat, df = sev_rf_df)
# 
# saveRDS(sev_rf, here("results", "sev_rf.rds"))

Plot model performance heatmap (severity)

sev_plsda <- readRDS(here("results", "sev_plsda.rds"))
sev_rf <- readRDS(here("results", "sev_rf.rds"))
col_names <- intersect(colnames(sev_rf$df), colnames(sev_plsda$df))
panel_names <- c("all", "panCancer", "UCSC_isoforms", "UCSC", "Ensembl", "Trinity")
auc <- rbind(sev_rf$df[, col_names],
             sev_plsda$df[, col_names]) %>% 
  filter(stat == "AUC.mean") %>% 
  dplyr::select(-stat) %>% 
  mutate(model_panel = paste(model, panel, sep="_")) %>% 
  dplyr::select(-c(model, panel)) %>% 
  spread(model_panel, value)

auc2 <- auc[, -c(1:4)]
classifer <- factor(sapply(strsplit(colnames(auc2), "_"), function(i) i[[1]]), 
                    c("PLSDA", "RF"))
colnames(auc2) <- sapply(strsplit(colnames(auc2), "_"), function(i) i[[2]])
row_ha <- rowAnnotation(sampletype=auc$sampletype,
                        comparison=auc$comparison, sex=auc$sex,
                        col = list(sampletype = c("airway"="#DEEBF7","BALF"="#9ECAE1","induced sputum"="#4292C6", "blood" = "red"),
                                   comparison = c("healthyControls_vs_moderateAsthma"="#E69F00", "healthyControls_vs_severeAsthma"="#56B4E9", "moderateAsthma_vs_severeAsthma"="#009E73"),
                                   sex = c("F"="#80CDC1","M"="#35978F","M+F"="#01665E")))

h2 <- Heatmap(auc2, column_split = classifer,
        right_annotation = row_ha, 
        cluster_columns = TRUE,
        border = TRUE, name="AUC",
    cell_fun = function(j, i, x, y, width, height, fill) {
        if(auc2[i, j] > 0.9) {
          grid.text("***", x, y, gp = gpar(fontsize = 15))
        } else if(auc2[i, j] > 0.8) {
          grid.text("**", x, y, gp = gpar(fontsize = 15))
        } else if(auc2[i, j] > 0.7) {
          grid.text("*", x, y, gp = gpar(fontsize = 15))
        }
})
h2

Summarize model performance table (severity)

sevtable <- rbind(sev_rf$df[, col_names],
             sev_plsda$df[, col_names]) %>% 
  mutate(value = signif(value, 2)) %>%  
  filter(stat == "AUC.mean") %>% 
  spread(model, value) %>% 
  filter(PLSDA > 0.7) %>% 
  filter(RF > 0.7)
write.csv(sevtable, here::here("results", "sev_models_perfs.csv"))

sevtable %>% 
  group_by(sampletype, comparison, sex) %>% 
  summarise(count = n()) %>% 
  spread(sampletype, count)

## # A tibble: 9 × 6
## # Groups:   comparison [3]
##   comparison                        sex   airway  BALF blood `induced sputum`
##   <chr>                             <chr>  <int> <int> <int>            <int>
## 1 healthyControls_vs_moderateAsthma F          5    NA    NA               NA
## 2 healthyControls_vs_moderateAsthma M          2     5    NA                2
## 3 healthyControls_vs_moderateAsthma M+F        5     4    NA               NA
## 4 healthyControls_vs_severeAsthma   F          5     6    NA                3
## 5 healthyControls_vs_severeAsthma   M          4     6     3                5
## 6 healthyControls_vs_severeAsthma   M+F        6     6     3                5
## 7 moderateAsthma_vs_severeAsthma    F         NA     6    NA                2
## 8 moderateAsthma_vs_severeAsthma    M         NA     6    NA                1
## 9 moderateAsthma_vs_severeAsthma    M+F       NA     6    NA                5

Compile feature importance + rank summaries

selectcols <- intersect(colnames(sev_plsda$feat), colnames(sev_rf$feat))
sevfeat <- rbind(sev_plsda$feat[, selectcols], 
                 sev_rf$feat[,selectcols]) %>% 
  right_join(sevtable, by=c("gse", "comparison", "panel", "sex", "sampletype")) %>% 
  dplyr::select(-c(stat, PLSDA, RF, gse)) %>% 
  group_by(comparison, panel, sex, model, sampletype) %>%
  mutate(rank_pct = percent_rank(importance))

exacer_rank <- exacerfeat %>%
  group_by(feature, comparison) %>%
  summarise(
   avg_rank = mean(rank_pct, na.rm = TRUE),
   sd_rank = sd(rank_pct, na.rm = TRUE),
   .groups   = "drop"
  )
sev_rank <- sevfeat %>%
  group_by(feature, comparison, sampletype) %>%
  summarise(
   avg_rank = mean(rank_pct, na.rm = TRUE),
   sd_rank = sd(rank_pct, na.rm = TRUE),
    .groups   = "drop"
  )

Pathway annotation + pathway barplots (assigned/unassigned)

# sev_rank is your tibble with feature, avg_rank, sd_rank

# pick a KEGG library available in Enrichr
dbs <- enrichR::listEnrichrDbs()
kegg_db <- dbs$libraryName[grepl("KEGG", dbs$libraryName)][1]
kegg_db

## [1] "KEGG_2013"

# e.g. "KEGG_2021_Human" (depends on what's available)

# run enrichr
db <- "GO_Biological_Process_2025"
enr <- enrichR::enrichr(latephase_biomarkers$all, databases = db)

## Uploading data to Enrichr... Done.
##   Querying GO_Biological_Process_2025... Done.
## Parsing results... Done.

kegg <- enr[[db]]

# keep significant-ish terms (tune as you like)
kegg_sig <- kegg %>%
  filter(Adjusted.P.value <= 0.1) %>%
  arrange(Adjusted.P.value)

# parse the "Genes" column from enrichr (overlapping genes per pathway)
gene_path_long <- kegg_sig %>%
  dplyr::select(Pathway = Term, padj = Adjusted.P.value, Genes) %>%
  mutate(Genes = str_split(Genes, pattern = ";\\s*")) %>%
  unnest(Genes) %>%
  dplyr::rename(feature = Genes)

# assign each gene to ONE pathway:
# (the pathway with smallest adjusted p among those containing the gene)
gene2path <- gene_path_long %>%
  group_by(feature) %>%
  slice_min(order_by = padj, n = 1, with_ties = FALSE) %>%
  ungroup()

# attach pathway to your ranking table
exacer_annot <- exacer_rank %>%
  left_join(gene2path %>% dplyr::select(feature, Pathway), by = "feature") %>%
  mutate(Pathway = ifelse(is.na(Pathway), "Unassigned", Pathway)) %>% 
  mutate(sampletype = "PBMCs") %>% 
  mutate(comparison = factor(comparison, c("Exacer vs. Quiet (Moderate Persistent)", "Exacer vs. Quiet (Severe Persistent)", "Exacer vs. followup (Moderate Persistent)", "Exacer vs. followup (Severe Persistent)")))
exacer_annot %>% head()

## # A tibble: 6 × 6
##   feature comparison                         avg_rank sd_rank Pathway sampletype
##   <chr>   <fct>                                 <dbl>   <dbl> <chr>   <chr>     
## 1 ABHD5   Exacer vs. Quiet (Severe Persiste…   0.320   0.128  Negati… PBMCs     
## 2 ABHD5   Exacer vs. followup (Moderate Per…   0.0979  0.0837 Negati… PBMCs     
## 3 ABHD5   Exacer vs. followup (Severe Persi…   0.798   0.0752 Negati… PBMCs     
## 4 AHCTF1  Exacer vs. Quiet (Severe Persiste…   0.675   0.0995 Unassi… PBMCs     
## 5 AHCTF1  Exacer vs. followup (Moderate Per…   0.545   0.216  Unassi… PBMCs     
## 6 AHCTF1  Exacer vs. followup (Severe Persi…   0.193   0.0829 Unassi… PBMCs

# attach pathway to your ranking table
sev_annot <- sev_rank %>%
  left_join(gene2path %>% dplyr::select(feature, Pathway), by = "feature") %>%
  mutate(Pathway = ifelse(is.na(Pathway), "Unassigned", Pathway))
sev_annot %>% head()

## # A tibble: 6 × 6
##   feature comparison                        sampletype  avg_rank sd_rank Pathway
##   <chr>   <chr>                             <chr>          <dbl>   <dbl> <chr>  
## 1 ABHD5   healthyControls_vs_moderateAsthma BALF           0.979  0.0180 Negati…
## 2 ABHD5   healthyControls_vs_moderateAsthma airway         0.293  0.187  Negati…
## 3 ABHD5   healthyControls_vs_moderateAsthma induced sp…    0.340  0.256  Negati…
## 4 ABHD5   healthyControls_vs_severeAsthma   BALF           0.704  0.173  Negati…
## 5 ABHD5   healthyControls_vs_severeAsthma   airway         0.291  0.191  Negati…
## 6 ABHD5   healthyControls_vs_severeAsthma   blood          0.694  0.272  Negati…

Assemble multi-panel Figure 4

p1_unassigned <- plot_varimp_pathways(
  exacer_annot,
  top_n = 30,
  sum_threshold = 1.5,
  include_unassigned = TRUE
) + theme(legend.position = "top") +
  scale_fill_manual(values = c("Exacer vs. Quiet (Moderate Persistent)"="#DEEBF7", "Exacer vs. Quiet (Severe Persistent)"="#9ECAE1", "Exacer vs. followup (Moderate Persistent)"="#4292C6", "Exacer vs. followup (Severe Persistent)"="#084594"))
p1_unassigned

p1_assigned <- plot_varimp_pathways(
  exacer_annot,
  top_n = 20,
  sum_threshold = 1.5,
  include_unassigned = FALSE
) + theme(legend.position = "top") +
  scale_fill_manual(values = c("Exacer vs. Quiet (Moderate Persistent)"="#DEEBF7", "Exacer vs. Quiet (Severe Persistent)"="#9ECAE1", "Exacer vs. followup (Moderate Persistent)"="#4292C6", "Exacer vs. followup (Severe Persistent)"="#084594"))
p1_assigned

p2_unassigned <- plot_varimp_pathways(
  sev_annot,
  top_n = 10,
  sum_threshold = 2,
  include_unassigned = TRUE
) + theme(legend.position = "top") +
  scale_fill_manual(values = c("healthyControls_vs_moderateAsthma"="#E69F00", "healthyControls_vs_severeAsthma"="#56B4E9", "moderateAsthma_vs_severeAsthma"="#009E73"))
p2_unassigned

p2_assigned <- plot_varimp_pathways(
  sev_annot,
  top_n = 10,
  sum_threshold = 2,
  include_unassigned = FALSE
) + theme(legend.position = "top") +
  scale_fill_manual(values = c("healthyControls_vs_moderateAsthma"="#E69F00", "healthyControls_vs_severeAsthma"="#56B4E9", "moderateAsthma_vs_severeAsthma"="#009E73"))
p2_assigned

ggsave(here("results", "Figure4b1.png"), plot = p1_unassigned, width = 3, height = 5)
ggsave(here("results", "Figure4b2.png"), plot = p1_assigned, width = 12, height = 5)
ggsave(here("results", "Figure4d1.png"), plot = p2_unassigned, width = 10, height = 5)
ggsave(here("results", "Figure4d2.png"), plot = p2_assigned, width = 10, height = 5)

save panels of Figure 4

library(grid)
library(patchwork)
library(ComplexHeatmap)

g1 <- grid.grabExpr(draw(h1, merge_legends = FALSE))
g2 <- grid.grabExpr(draw(h2, merge_legends = FALSE))
ggsave(here("results", "Figure4a.png"), plot = g1, width = 10, height = 5)
ggsave(here("results", "Figure4b.png"), plot = p1_assigned, width = 10, height = 5)
ggsave(here("results", "Figure4c.png"), plot = g2, width = 10, height = 7)
ggsave(here("results", "Figure4d.png"), plot = p2_assigned, width = 10, height = 7)

Check top transcripts in male panel

male_features <- exacerfeat %>% 
  ungroup() %>% 
  group_by(feature, comparison) %>% 
  filter(sex == "M") %>% 
  summarise(avg = mean(rank_pct)) %>% 
  arrange(desc(avg)) %>% 
  ungroup() %>% 
  group_by(comparison) %>% 
  dplyr::slice(1:2) %>%
  mutate(
    severity = sub("^.*\\((.*)\\)\\s*$", "\\1", comparison)       # text inside ()
  )

plots <- mapply(function(x, y){
    res = plot_gene_sex_lme(gene = x,
           severity = y,
           geoPanelGenes = geoPanelGenes,
           phenoDataList = phenoDataList)
  res$plot
}, x = male_features$feature, y = male_features$severity)


male_plots <- plot_grid(plotlist = plots)
ggsave(here("results", "male_specific_biomarkers.png"), male_plots,
       width = 10, height = 7)
male_plots

sessionInfo

sessionInfo()

## R version 4.5.1 (2025-06-13)
## Platform: x86_64-apple-darwin20
## Running under: macOS Ventura 13.6.7
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: America/Vancouver
## tzcode source: internal
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] patchwork_1.3.2       future.apply_1.20.0   future_1.67.0        
##  [4] ranger_0.17.0         pROC_1.19.0.1         cowplot_1.2.0        
##  [7] UpSetR_1.4.0          ggrepel_0.9.6         enrichR_3.4          
## [10] here_1.0.2            ComplexHeatmap_2.26.0 mixOmics_6.34.0      
## [13] lattice_0.22-7        MASS_7.3-65           limma_3.66.0         
## [16] nlme_3.1-168          lubridate_1.9.4       forcats_1.0.1        
## [19] stringr_1.6.0         dplyr_1.1.4           purrr_1.1.0          
## [22] readr_2.1.6           tidyr_1.3.1           tibble_3.3.0         
## [25] ggplot2_4.0.1         tidyverse_2.0.0      
## 
## loaded via a namespace (and not attached):
##   [1] RColorBrewer_1.1-3  rstudioapi_0.17.1   jsonlite_2.0.0     
##   [4] shape_1.4.6.1       magrittr_2.0.4      estimability_1.5.1 
##   [7] magick_2.9.0        farver_2.1.2        nloptr_2.2.1       
##  [10] rmarkdown_2.30      GlobalOptions_0.1.2 ragg_1.5.0         
##  [13] vctrs_0.6.5         Cairo_1.7-0         minqa_1.2.8        
##  [16] rstatix_0.7.3       htmltools_0.5.8.1   curl_7.0.0         
##  [19] broom_1.0.10        janeaustenr_1.0.0   Formula_1.2-5      
##  [22] sass_0.4.10         parallelly_1.45.1   bslib_0.9.0        
##  [25] tokenizers_0.3.0    pbkrtest_0.5.5      plyr_1.8.9         
##  [28] emmeans_2.0.1       cachem_1.1.0        commonmark_2.0.0   
##  [31] igraph_2.2.1        lifecycle_1.0.4     iterators_1.0.14   
##  [34] pkgconfig_2.0.3     Matrix_1.7-3        R6_2.6.1           
##  [37] fastmap_1.2.0       rbibutils_2.4       clue_0.3-66        
##  [40] numDeriv_2016.8-1.1 digest_0.6.37       tidytext_0.4.3     
##  [43] colorspace_2.1-2    rARPACK_0.11-0      S4Vectors_0.48.0   
##  [46] rprojroot_2.1.1     RSpectra_0.16-2     textshaping_1.0.4  
##  [49] ellipse_0.5.0       SnowballC_0.7.1     ggpubr_0.6.2       
##  [52] WriteXLS_6.8.0      labeling_0.4.3      timechange_0.3.0   
##  [55] abind_1.4-8         httr_1.4.7          compiler_4.5.1     
##  [58] withr_3.0.2         doParallel_1.0.17   backports_1.5.0    
##  [61] S7_0.2.0            BiocParallel_1.44.0 carData_3.0-5      
##  [64] ggsignif_0.6.4      rjson_0.2.23        corpcor_1.6.10     
##  [67] tools_4.5.1         glue_1.8.0          gridtext_0.1.5     
##  [70] cluster_2.1.8.1     reshape2_1.4.4      generics_0.1.4     
##  [73] gtable_0.3.6        tzdb_0.5.0          hms_1.1.4          
##  [76] car_3.1-3           xml2_1.4.1          utf8_1.2.6         
##  [79] BiocGenerics_0.56.0 foreach_1.5.2       pillar_1.11.1      
##  [82] markdown_2.0        circlize_0.4.16     splines_4.5.1      
##  [85] ggtext_0.1.2        tidyselect_1.2.1    knitr_1.50         
##  [88] reformulas_0.4.2    gridExtra_2.3       litedown_0.8       
##  [91] IRanges_2.44.0      stats4_4.5.1        xfun_0.54          
##  [94] statmod_1.5.1       matrixStats_1.5.0   stringi_1.8.7      
##  [97] yaml_2.3.12         boot_1.3-31         evaluate_1.0.5     
## [100] codetools_0.2-20    cli_3.6.5           xtable_1.8-4       
## [103] systemfonts_1.3.1   Rdpack_2.6.4        jquerylib_0.1.4    
## [106] Rcpp_1.1.0          globals_0.18.0      coda_0.19-4.1      
## [109] png_0.1-8           parallel_4.5.1      lme4_1.1-37        
## [112] listenv_0.10.0      mvtnorm_1.3-3       lmerTest_3.1-3     
## [115] scales_1.4.0        crayon_1.5.3        GetoptLong_1.0.5   
## [118] rlang_1.1.6